High I/O causes drives to disappear, garbled displays, USB malfunctio

This past week has been a weird one. Both hardware and software has been erratic. Every time it acts up I've noticed I've either been installing software, transferring a lot of files, or even I/O operations through USB. So far it seems like it may have start ed with some IO Controller. But has since grown to many other areas,because I think, and I may be wrong, that only hardware issues could cause crashes like the ones described below.

I have 5 Drives in total. 3 Main ones and 2 for backup. Listed below with Drive letter, Model, Power on Time (days), and purpose:
C:\ 256GB Samsung 840 Evo (412) - Windows Installation
D:\ 256GB Crucial m4 (1021) - Pagefile, TEMP, and folders that C:\ Symlinks to using Link Shell Extensions.
M:\ 4.0TB HGST Desktar (250) - Media drive. Most user folders symlinked from here.
E:\ 1.0TB Samsung Spinpoint (1446) - Old Media drive. Just finished moving the last files to M so that I could use it for backup, due to the recent issues.
Z:\ 500GB Samsung Spinpont (2614d) WindowsBackup. Can restore from periods:1/30/2013-5/30/2013 and 10/17/2013-8/27/2014.

Some of the things I've found odd leading up to these events are:
1.) Some folders open up really really slowly sometimes for no reason.
2.) Sometimes when I open "My Computer" drive M: will suddenly appear, a second later it will show as full. Then windows begins to evaluate the drives usage and I can observe it slowly detecting the available free space by watching the space available bar. .

1. 9/26/15. I was noticing some odd program behavior and decided I should get around to actually backing up my important files. While copying user files to E: the system began acting up. Mouse movements became jerky as if the system was entering a blocking interrupt procedure. I stopped the copy. Below is what the logs say. I also notice this same issue had happened 3 days prior and several other times since June to drive M:
   
   volsnap: The shadow copies of volume E: were deleted because the shadow copy storage could not grow in time. Consider reducing the IO load on the system or choose a shadow copy storage volume that is not being shadow copied.
   What does that even mean? Could hardlink clones have something to do with this? I wasn't sure what they were so went ahead and created them once to check out what they're all about and decided I didn't like them. I'm thinking I may have not of "delinked" them properly before shuffling files around D, E, and M. Is that even possible?
   
2. 10/3/15 5:29PM. It was taking forever to open my Downloads folder. That coupled with the errors I seen earlier made me think that maybe I should move files off Hard Disks and onto SSD drive D:. From M: I tried to move Downloads and My Documents to D:. In the middle of doing this windows made that "dun-dun" sound and drive D just disappears. The system was soon restarted
   
   volsnap: The shadow copies of volume D: were aborted because of an IO failure on volume D:
   Ntfs: The system failed to flush data to the transaction log. Corruption may occur.
   Application popup: Windows - Delayed Write Failed : Exception Processing Message 0xc0000222 Parameters 0x000007FEFD25718C 0x000007FEFD25718C 0x000007FEFD25718C 0x000007FEFD25718C
3. 10/3/15 7:04PM. Still at it trying to duplicate my most important files across drives D, E, and M when I hear the "dun-dun" sound again. This time drive E drops offline .
   
   volsnap: The shadow copies of volume E: were aborted because volume E:, which contains shadow copy storage for this shadow copy, was force dismounted.
4. 10/4/15 7:38PM. I don't remember what was going on here. I'm pretty sure this is the "My Computer" issue I talked about earlier where drive M will just appear and then initialize.
   
   Microsoft-Windows-UserPnp: Driver Management has concluded the process to add Service volsnap for Device Instance ID STORAGE\VOLUME\{2D21F9A7-A425-11E4-8962-806E6F6E6963}#000002A914400000 with the following status: 0.
   Microsoft-Windows-UserPnp: Driver Management concluded the process to install driver FileRepository\volume.inf_amd64_neutral_df8bea40ac96ca21\volume.inf for Device Instance ID STORAGE\VOLUME\{2D21F9A7-A425-11E4-8962-806E6F6E6963}#000002A914400000 with the following status: 0x0.
   VSS:Volume Shadow Copy Service error: Error calling a routine on a Shadow Copy Provider {b5946137-7b9f-4925-af80-51abd60b20d5}. Routine details IVssSnapshotProvider::IsVolumeSupported() failed with 0x8000ffff [hr = 0x8000ffff, Catastrophic failure].
5. 10/5/15 7:50AM. Was working on a CSCE project using Altera Quartus II 12sp2 and NIOS II EDA for Eclipse Helios developing on a Cyclone II FPGA. I Was in the middle of flashing the board I believe when this happened out of the blue. The logs don't tell me anything. There isn't anything logged from 7:31:02AM to 7:50:48.
   
   
   EventLog: The previous system shutdown at 7:46:44 AM on ‎10/‎5/‎2015 was unexpected.
6. 10/5/15 11:33:28AM. Eventually I thought maybe I'd try a later version of Quartus, version 15. It's not compatible with my FPGA but I wanted to see if the newer NIOS II EDA for Eclipse component would work with my older chipset. Right after the system created a restore point before installing the software suite, below happened. While this was going on I tried to launch procexp64 but it crashed. After that I was just trying to get things saved and the computer restarted.
   
   
   Information: 11:33:23AM Successfully created restore point (Process = D:\HARDLI~1\C\altera\15.0\VCREDI~2.EXE /q /norestart; Description = Microsoft Visual C++ 2013 Redistributable (x64) - 12.0.21005).
   Ntfs: 11:33:28AM The system failed to flush data to the transaction log. Corruption may occur.
   volsnap: 11:33:28AM The shadow copies of volume D: were aborted because of an IO failure on volume D:.
   Application Error: 11:34:04AM Faulting application name: notepad++.exe, version: 6.8.3.0, time stamp: 0x55e8c674, Exception code: 0xc0000006,Fault offset: 0x000fb87c, There is a problem with: the disk that the file is stored on, the storage drivers installed on this computer; or the disk is missing.
   Application Error: 11:36:28AM Faulting application name: procexp64.exe, version: 16.5.0.0, time stamp: 0x55503597, Faulting module name: ntdll.dll, version: 6.1.7601.18933, time stamp: 0x55a6a196, The application was unable to start correctly (0xc0000006)
   Application Popup: 11:37:25AM Application popup: Windows - Delayed Write Failed : Exception Processing Message 0xc0000222 Parameters 0x000007FEFCB4718C 0x000007FEFCB4718C 0x000007FEFCB4718C 0x000007FEFCB4718C, \Device\HarddiskVolume7\HardLinks\C\altera\13 .. 86_1.1.300.v20150602-1417\META-INF\MANIFEST.MF
   USER32: 11:38:22AM The attempt by user to restart/shutdown computer failed
   And then for the big finale! DISPLAY CORRUPTION and crash
   Kernel-Power: 11:41:17AM The system has rebooted without cleanly shutting down first. This error could be caused if the system stopped responding, crashed, or lost power unexpectedly.
   volsnap: 11:41:47AM The shadow copies of volume D: were aborted during detection because a critical control file could not be opened.
7. 10/6/15 Today the system logs are polluted with the following errors, literally thousands of these same messages, but so far no hard crashes today. Also I've never actually gotten an error popup like the logs say I have. The errors don't seem to change even though there are so many. In order:
   
   atapi: The driver detected a controller error on \Device\Ide\IdePort1.
   Disk: The device, \Device\Harddisk1\DR1, is not ready for access yet.
   volsnap: The shadow copies of volume D: were aborted because of an IO failure on volume D:.
   Disk: An error was detected on device \Device\Harddisk1\DR1 during a paging operation.
   Ntfs: The system failed to flush data to the transaction log. Corruption may occur.
   Application Popup: Windows - Delayed Write Failed : Exception Processing Message 0xc0000222 Parameters 0x000007FEFCE2718C 0x000007FEFCE2718C 0x000007FEFCE2718C 0x000007FEFCE2718C
   Ntfs: The description for Event ID 50 from source Ntfs cannot be found. Either the component that raises this event is not installed on your local computer or the installation is corrupted.
   VDS Basic Provider: Unexpected failure. Error code: 2@01050005

When trying to use Windows Backup. I now get this message.

[Main Instruction]
Check your backup
[Content]
Windows Backup failed while trying to read from the shadow copy on one of the volumes being backed up. Please check in the event logs for any relevant errors.
[^] Hide Details [Try to run backup again] [Change backup settings] [Cancel]
[Expanded Information]
Backup time: 8/27/2014 4:33 PM
Backup location: WindowsBackup (Z:)
Error code: 0x81000037

So yea, whats going on? My hard disks keep disconnecting and there seems to be an issue with Shadow Volumes. It just dropped drive D again a bit ago but it wasn't in use so I was able to go into device manager and press "refresh devices", and then it redetected and mounted drive D.

Also I believe there is a connection between these events and having the Cyclone II FPGA development board plugged in through USB. For instance, if the board ****s up, sometimes it will also take another USB peripheral with it. Like the other day my keyboard stopped working and I had to completely disconnect the computer from power to get it working again. Since then, the USB port that that dev board was plugged into no longer works properly. Any device I plug into it, the Dev Board, a USB drive, my Phone, windows will try to detect it and then say failed to install device driver. If I then use a different USB port the drivers install fine.

The Motherboard and chipset for this PC is ASRock z77 Xtreme4

EDIT: HERES ANOTHER ONE IM POSTING IN REAL TIME!
[Window Title]
You are about to be logged off
[Main Instruction]
Windows must now restart because the DCOM Server Process Launcher service terminated unexpectedly
[Close]

Posting from mobile now. It restarted and I had chkdsk schedules set for every drive. See how that goes. Pretty disappointed that my file histories are gone. That the whole reason for the symlinks. So I can dedicate 50gb to volume shadow storage to only my user files on D without having windows eating into it. .

My question though is what should I do? I can't just reinstall windows without first ruling out hardware. Also have way too many important programs, settings, and configs that I would not want to or even could not set up again because of educational licensing.

Please fill out your system specs so that we can help you better.

I'm starting to think that the Crucial M4 is dieing. I've moved the systems TEMP folder and page file off it after the earlier two crashes. Once this full backup is completed I was planning on stress testing it to see if it will trigger a crash.

So far I've been moving the files off it without an issue, but I'm using 7-zip to minimize file IO operations on the target drive so that the write is a single long sequential write instead of random.

Coincidence?

Code:

CPU:           Intel Core i7-3770K (Ivy Bridge-DT, E1)
               3500 MHz (35.00x100.0) @ 4202 MHz (42.00x100.1)
Motherboard:   ASRock Z77 Extreme4
Chipset:       Intel Z77 (Panther Point DH)
Memory:        16384 MBytes @ 933 MHz, 9.0-10-10-27
               - 8192 MB PC12800 DDR3 SDRAM - Corsair CMZ16GX3M2A1600C10
               - 8192 MB PC12800 DDR3 SDRAM - Corsair CMZ16GX3M2A1600C10
Graphics:      AMD Radeon HD 7950
               ATI/AMD Radeon HD 7950/R9 280, 3072 MB GDDR5 SDRAM
Drive:         Samsung SSD 840 EVO 250GB, 244.2 GB, Serial ATA 6Gb/s @ 6Gb/s
Drive:         M4-CT256M4SSD2, 250.1 GB, Serial ATA 6Gb/s @ 6Gb/s
Drive:         SAMSUNG HD501LJ, 488.4 GB, Serial ATA 3Gb/s
Drive:         SAMSUNG HD103SJ, 976.8 GB, Serial ATA 3Gb/s
Drive:         HGST HDN724040ALE640, 3907.0 GB, Serial ATA 6Gb/s @ 6Gb/s
Drive:         HL-DT-ST DVD-RAM GH22NS30, DVD+R DL
Sound:         ATI/AMD Tahiti - High Definition Audio Controller
Sound:         Creative SB Recon3D PCIe Audio Controller
Network:       VirtualBox Host-Only Ethernet Adapter
Network:       802.11n USB Wireless LAN Card
OS:            Microsoft Windows 7 Professional (x64) Build 7601

A full report generated by HWiNFO64 can be found here:
https://dl.dropboxusercontent.com/u/...4/HWiNFO64.HTM

EDIT: I actually have a SB Soundblaster Z. Because it was reported wrong I just updated the driver, thinking maybe something was wrong there. The computer started up really really slow and at one point I thought I was going to have to hard reset it because it wasn't responding to inputs. I looked at the eventlog once started:

volsnap: The shadow copies of volume C: were deleted because the shadow copy storage could not grow in time. Consider reducing the IO load on the system or choose a shadow copy storage volume that is not being shadow copied.

This drive has been completely unaffected until this point. The only thing that changed was that I moved the PageFile and Temp directory back onto it because I thought the Crucial M4 was on its last leg. I now have shadow copy completely disabled and the PageFile disabled.

I'd already ordered a 500GB Samsung 850 Evo that's supposed to be here Sunday (they're going for 160 bucks a pop on Amazon right now). I've also had a licensed Win10 EDU edition that's been sitting in my desk for a while and I suppose its finally time to give it a go.

If the problem's not Windows... I don't know what to do. I can't shake the feeling that it's a hardware issue because of the severity and abruptness of the crash and you'd think windows would throw a bugcheck at least. It'll run games like BF4 all day, Prime95 all day, Memtest all day, but as soon as I copy a bunch of little files from one drive to the next it all goes to hell.

I think I'll order a PCIe Sata controller for all non bootable drives as a precaution.

I wonder if your motherboard is going south on you? That would cause some of the problems that you are having.

And also, the Cyclone board borking USB ports... Is that a genuine Altera Cyclone board, or a Chinese knockoff? I've blown out USB ports with those knockoff boards in the past. It might be that the damage was not limited to your USB port.

terasIC boards are genuine. There's no problem there. Or there shouldn't be. If it's borking ports when it goes nutty, though, I think I would put in a ticket with terasIC and see what they think of the issue.

But that's a separate problem...

As far as your PCH voltage goes, I can't advise. I'm unfamiliar with Intel boards on that detail level. Sorry.

EDIT: Actually, I just looked it up. If you aren't overclocking, you shouldn't need to adjust PCH, but you could try bumping it up just a smidge and see if it stabilizes your system. I wouldn't raise it by too much though.

Just some information.

Vcore, VTT, DRAM, PLL, PCH - Voltages Explained - Core i7, i5, i3

Platform Controller Hub (PCH)

The PCH voltage feeds the p55 chipset on the motherboard, which is responsible for talking with all of the peripherals on your computer, such as USB devices, hard drives, and any add-on cards--except for the video cards--which now talk directly to the PCI-Express controller integrated into the CPU.
You probably won't need to mess with this voltage, but I just mentioned it because some people say that they needed to increase it from its default of 1.05 V to 1.1 V to achieve stability. I've never needed to mess with this though, so I'd only play with it as a last resort.

That USB port that I said stopped working is working now.

I upped the PCH voltage then ran the file benchmark using HD Tune Pro on the M4. This is how far it got before it dropped offline. I had to go into device manager and "Scan For Hardware Changes" to bring it back online.
This is how far it got:
https://i.imgur.com/7BdJtbi.png

Kind of regretting doing it because now I can't even do the 7-zip trick to get files off it. I can do about 2GB of reads before it drops offline. I'm starting to think the Crucial M4 is the source of all the problems again. Every SMART attribute is still good and it shows 94% life left.
In the last 7 days it's had:

• 45,010 Disk An error was detected on device \Device\Harddisk1\DR1 during a paging operation.
• 61 NTFS The system failed to flush data to the transaction log. Corruption may occur.
• 3 Atapi The driver detected a controller error on \Device\Ide\IdePort1.
• 5 Disk: The device, \Device\Harddisk1\DR1, is not ready for access yet.

Got the Samsung 850 500GB today and a PCIe 4 port sata controller. So far I've been to lazy to do anything with them yet.

Right now I'm running multiple instances of that File Benchmark on the other disks to see if anything comes up. Resource Monitor says I'm doing 250-750MB/s of IO all together and there's no error yet. My mouse will periodically lock up for a second or so every so often though.

EDIT: Apparently it was a fluke. It's working now? https://i.imgur.com/nK3Q2CG.png