Bad Sectors

What is on Disk0? Ubuntu? It has no System flag so I assume if it's a bootable OS it is booting via C. If there's no OS on Disk0 I would move the Win7 HD there, making sure it remains set to boot first in BIOS setup.
No, it is my old installation of W7. I intended to reformat the drive, once I was sure that there is nothing on it that I need, but haven't got around to it yet.
The WDC 2tb external lettered M is not showing on map, but should not be Active. Where this can be a problem is if it has previously been bootsected and is interfering with boot. I would mark it Inactive using Diskpart from Elevated Command Prompt: Partition - Mark as Active (Method Two)

The Disk Check and definitive HD testing is more important at this point.

It isn't showing on the map, because it would have to be scrolled up, but I did check and found that both it and drive 0 are marked active, so I will change that.
 

My Computer

Computer Manufacturer/Model Number
DIY
OS
W7x64 Pro, SuSe 12.1/** W7 x64 Pro, XP MCE
CPU
Phenom II 1090T w/Noctua NH-D14 /**4400+ X2 w/CM Hyper TX 3
Motherboard
ASRock 890FX Deluxe 4/**A8N-SLI
Memory
2 x 2GB Patriot PGS34g1600LLKA/**4x1GB Corsair VS
Graphics Card(s)
EVGA GTX460 SC/**EVGA 8800GTS
Sound Card
Asus Xonar D2X/**Xonar D1
Monitor(s) Displays
Acer X233H, Dell E152FPc /**LG M237-WD
Screen Resolution
1920x1080 & 1024x768/**1980x1080
Hard Drives
WDC 2TB, 1.5TB, 1TB, 500GB,Seagate 500GB , Maxtor 80GB /**500GB Seagate & WDC 1TB Black
PSU
CM RS600 w/ APC BX1000G/**Antec 500 TP w/ APC BX1000
Case
HAF922/**Antec 1040IIB
Cooling
3x200mm, 1x140 and 1x120mm/**5x80mm fans
Keyboard
Logitech Media USB/**Saitek Eclipse
Mouse
Cordless Trackman Wheel/**Ditto
Internet Speed
3.3Mbps
Other Info
SB 560 5.1 w/ Sennheiser RS140/**Creative T20 speakers, Dvico FusionHDTV7 Gold RT, Cisco E3000, HP 5510V AIO, Linksys E3000, Belkin F5U237 hub and **F5D8055 adapter
(** = 2nd rig)
Did the new WIn7 installation create a Dual Boot with the old one via System boot files on C? If so deleting it in Disk Management or Diskpart may not remove the Menu entry. In that case install EasyBCD 2.1 to Edit Boot Menu, highlight old listing to Delete, Save.

Do you happen to know if the External marked Active was ever bootsected to boot for some reason, perhaps to install Windows? If so, it could be interfering with your boot. Marking Inactive might help but you may also need to move the data off to wipe it of boot code: Clean and Clean All with Diskpart Command
 
Did the new WIn7 installation create a Dual Boot with the old one via System boot files on C? If so deleting it in Disk Management or Diskpart may not remove the Menu entry. In that case install EasyBCD 2.1 to Edit Boot Menu, highlight old listing to Delete, Save.
No, I installed W7 on the new drive, while all other drives were disconnected, so it should not have anything to do with the boot menu.
Do you happen to know if the External marked Active was ever bootsected to boot for some reason, perhaps to install Windows? If so, it could be interfering with your boot. Marking Inactive might help but you may also need to move the data off to wipe it of boot code: Clean and Clean All with Diskpart Command
Bootsected? That is a new term for me, so I had to Google it. Neither of the external drives were ever used for an OS, and I thought that I had removed that active flag previously, but I can't be certain. In any case, since the drive has never been used for anything except storage, I don't think that is an issue.

I did finish check disk on drive T: and it did say that it had fixed a bad sector on it, but HD Tune still shows a damaged block on it. Before starting the scan, I checked the SMART data on it, and it had not changed at all. I guess as far as HD Tune is concerned, once there is a bad sector, there is always a bad sector. That again raises the question regarding drive M:, because as I was told, the SMART data on it says that there is one bad sector, plus one pending, just like drive T:, but the scan in HD Tune doesn't find anything to squawk about. It would seem that whatever is true for one drive, would be true for the other.

EDIT: I forgot to mention, that the bad sector repair had no effect on the boot problem. Therefore I think that the problem is either with the controller or the motherboard.
 

My Computer

Computer Manufacturer/Model Number
DIY
OS
W7x64 Pro, SuSe 12.1/** W7 x64 Pro, XP MCE
CPU
Phenom II 1090T w/Noctua NH-D14 /**4400+ X2 w/CM Hyper TX 3
Motherboard
ASRock 890FX Deluxe 4/**A8N-SLI
Memory
2 x 2GB Patriot PGS34g1600LLKA/**4x1GB Corsair VS
Graphics Card(s)
EVGA GTX460 SC/**EVGA 8800GTS
Sound Card
Asus Xonar D2X/**Xonar D1
Monitor(s) Displays
Acer X233H, Dell E152FPc /**LG M237-WD
Screen Resolution
1920x1080 & 1024x768/**1980x1080
Hard Drives
WDC 2TB, 1.5TB, 1TB, 500GB,Seagate 500GB , Maxtor 80GB /**500GB Seagate & WDC 1TB Black
PSU
CM RS600 w/ APC BX1000G/**Antec 500 TP w/ APC BX1000
Case
HAF922/**Antec 1040IIB
Cooling
3x200mm, 1x140 and 1x120mm/**5x80mm fans
Keyboard
Logitech Media USB/**Saitek Eclipse
Mouse
Cordless Trackman Wheel/**Ditto
Internet Speed
3.3Mbps
Other Info
SB 560 5.1 w/ Sennheiser RS140/**Creative T20 speakers, Dvico FusionHDTV7 Gold RT, Cisco E3000, HP 5510V AIO, Linksys E3000, Belkin F5U237 hub and **F5D8055 adapter
(** = 2nd rig)
When we create a flash/external HD installer, we apply bootsect /nt60 code which along with the Active flag enables it to boot. I shorthand that bootsected, tho neither are actual verbs. Sorry.

You can try changing Win7 HD to Disk0 to see if there's a difference with booting, and to keep it out of trouble during Repairs if another stray partition on a preceding HD gets marked Active.

We regularly get cases here where an external when plugged will interfere with booting, which are solved by either removing their active flag and/or moving their data off to wipe them of all code using Clean and Clean All with Diskpart Command
 
Since that external contains ~1000GBs of videos, I'm not anxious to move that data elsewhere. Besides, the boot problem is the same, regardless of which of the externals is powered up, even the one that wasn't flagged, so I doubt that it would do any good.
 

My Computer

Computer Manufacturer/Model Number
DIY
OS
W7x64 Pro, SuSe 12.1/** W7 x64 Pro, XP MCE
CPU
Phenom II 1090T w/Noctua NH-D14 /**4400+ X2 w/CM Hyper TX 3
Motherboard
ASRock 890FX Deluxe 4/**A8N-SLI
Memory
2 x 2GB Patriot PGS34g1600LLKA/**4x1GB Corsair VS
Graphics Card(s)
EVGA GTX460 SC/**EVGA 8800GTS
Sound Card
Asus Xonar D2X/**Xonar D1
Monitor(s) Displays
Acer X233H, Dell E152FPc /**LG M237-WD
Screen Resolution
1920x1080 & 1024x768/**1980x1080
Hard Drives
WDC 2TB, 1.5TB, 1TB, 500GB,Seagate 500GB , Maxtor 80GB /**500GB Seagate & WDC 1TB Black
PSU
CM RS600 w/ APC BX1000G/**Antec 500 TP w/ APC BX1000
Case
HAF922/**Antec 1040IIB
Cooling
3x200mm, 1x140 and 1x120mm/**5x80mm fans
Keyboard
Logitech Media USB/**Saitek Eclipse
Mouse
Cordless Trackman Wheel/**Ditto
Internet Speed
3.3Mbps
Other Info
SB 560 5.1 w/ Sennheiser RS140/**Creative T20 speakers, Dvico FusionHDTV7 Gold RT, Cisco E3000, HP 5510V AIO, Linksys E3000, Belkin F5U237 hub and **F5D8055 adapter
(** = 2nd rig)
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