Open the Command Prompt when the Installation DVD Loads and type the following commands.
chkdsk /r c:.etc until you get the message that the volume could not be opened for direct access. For any drives that do not give the message:
chkdsk /r d:
chkdsk /r e:
chkdsk /r f:
"Windows has checked the file system and found no problems"
run chkdsk again as above. In other words, if it says:
"Windows has made corrections to the file system"
after running the disk check, run the disk check again.
I realize you may only have one disk show up in Windows explorer, but you may have more than one disk through recovery options. This is because the system creates a hidden boot partition (which will be C: in recovery), you may have a recovery partition for your PC that is hidden (which will be D: in recovery), and you will have your primary Windows partition (which may be E: in recovery). A custom PC will likely have at least C: and D: to scan.
But first try fixing the BCD because it's likely damaged: Repair Windows BCD