Hard Drive Management Gone Haywire

If you can boot the installer stick but not see it in Explorer or Disk Mgmt then you have OS corruption. I'd get on the SFC /SCANNOW Command to see how bad it gets. If irreparable System Files you'll want a Repair Install.

But first ask yourself how close you have to a perfect Clean Reinstall - Factory OEM Windows 7 since you might want to invest in one now following these steps to get and keep a flawless install. A factory preinstall or lesser install cheats you of Win7 native performance.

gregrocker said:

If you can boot the installer stick but not see it in Explorer or Disk Mgmt then you have OS corruption. I'd get on the SFC /SCANNOW Command to see how bad it gets. If irreparable System Files you'll want a Repair Install.

But first ask yourself how close you have to a perfect Clean Reinstall - Factory OEM Windows 7 since you might want to invest in one now following these steps to get and keep a flawless install. A factory preinstall or lesser install cheats you of Win7 native performance.

I will do a SFC scan later, after my System Repair gets done.
As for Repair Install, I will only do at last resort.
For Clean Reinstall, that's a no-go for me. I've been advised that over 10 times here @SevenForums, but nope.avi :) Sorry, just a bit stubborn. Anyway, I'm getting a new PC very soon, so that'll be great for all these issues. But for the meantime, just want to get over this problem.

Oh snap.
System Repair has been running for 1.5 hours now.
HD activity indicator is lit up steadily.
What should I do? Just wait it out?

System Repair just finished.
The root cause was "The partition table does not have a valid System Partition".
Repair action: Partition table repair
Will reboot and see if everything's okay.

EDIT: When I restarted, it said that System Repair needed to run again. I will do that, but I booted up anyway. When I go to Disk Management, I see my data/system partition, plus the test partition I created. No sign of the unallocated space.

When I go to Device Manager, my USB flash drives show up there with a yellow hazard sign, and in the status, it says "Windows cannot load the device driver for this hardware. The driver may be corrupted or missing. (Code 39)"

I am running a SFC scan now, and will report back on the status. Also, I will re-run System Repair later.

EDIT 2:
This is last night's CHKDSK log.

Code:

Checking file system on C:
The type of the file system is NTFS.
Volume label is Hard Drive.

A disk check has been scheduled.
Windows will now check the disk.                         

CHKDSK is verifying files (stage 1 of 5)...
  206592 file records processed.                                          File verification completed.
  936 large file records processed.                                      0 bad file records processed.                                        0 EA records processed.                                              50 reparse records processed.                                       CHKDSK is verifying indexes (stage 2 of 5)...
  259118 index entries processed.                                         Index verification completed.
  0 unindexed files scanned.                                           0 unindexed files recovered.                                       CHKDSK is verifying security descriptors (stage 3 of 5)...
  206592 file SDs/SIDs processed.                                         Cleaning up 1158 unused index entries from index $SII of file 0x9.
Cleaning up 1158 unused index entries from index $SDH of file 0x9.
Cleaning up 1158 unused security descriptors.
Security descriptor verification completed.
  26264 data files processed.                                            CHKDSK is verifying Usn Journal...
  1132056 USN bytes processed.                                             Usn Journal verification completed.
CHKDSK is verifying file data (stage 4 of 5)...
Windows replaced bad clusters in file 91041
of name \SwSetup\Drivers\Video_P\Packages\Apps\CCC2\Help\fi\CCC-HE~1.MSI.
Windows replaced bad clusters in file 100174
of name \PROGRA~2\HEWLET~1\HP Setup\Images\HP\SEQUEN~1\GOCLIC~1\_GB17B~1.PNG.
Windows replaced bad clusters in file 112430
of name \Backups\EXTERN~1\GRADE4~1\July 13th, 2008\105.png.
  206576 files processed.                                                 File data verification completed.
CHKDSK is verifying free space (stage 5 of 5)...
  13329353 free clusters processed.                                         Free space verification is complete.
CHKDSK discovered free space marked as allocated in the volume bitmap.
Windows has made corrections to the file system.

 157286399 KB total disk space.
 103566460 KB in 119510 files.
    119752 KB in 26265 indexes.
         0 KB in bad sectors.
    282775 KB in use by the system.
     65536 KB occupied by the log file.
  53317412 KB available on disk.

      4096 bytes in each allocation unit.
  39321599 total allocation units on disk.
  13329353 allocation units available on disk.

Internal Info:
00 27 03 00 7a 39 02 00 93 6c 03 00 00 00 00 00  .'..z9...l......
9d 00 00 00 32 00 00 00 00 00 00 00 00 00 00 00  ....2...........
00 00 00 00 00 00 00 00 00 00 00 00 01 00 00 00  ................

Windows has finished checking your disk.
Please wait while your computer restarts.

Just did a SFC scan, it was clean, even in the CBS log.
Will do Startup Repair next.
EDIT: Am installing updates, will do Startup Repair right after.

So you know, in the first System Repair that I did, that it did a partition table repair that took 1 and a half hours? Well, I re-ran System Repair, and it did the partition table repair AGAIN, taking up another 1 and a half hours. So that means that I will NOT be running System Repair again unless it's needed.
What further action should I take?

Ok, so I messed around a bit, and completely screwed up mah system :P
I ran some variation of this command: bootsect /nt60 sys force, and now, when I boot, it gives me the message "No bootable device, insert boot device and press any key to continue."
Also, I realized that the filesystem was changed to RAW :P And I can't see any of mah files

Why would you run the bootsect command when there was no indication the boot files were problematic?

If you'd been patient we would have advised you based on your reports to test the HD before proceeding any further, using the maker's HD Diagnostic extended CD scan, followed by another Disk Check. The two repairs can either fix the HD or at least give you certainty about it's condition.

I would do that now before proceeding. If HD passes then confirm the Active partition is C and run Startup Repair - Run up to 3 Separate Times.
Partition - Mark as Active (Method Two)