A bit ago I struggled (for about 18hrs) after a root on one of my database servers gave me a blue screen saying the SAM file was corrupt. Well after many tries of chkdsk, fixdisk, windows repair, I finally found this option that fixed all the Windows boot files:
Boot from OS install disk Select next after making sure the language options are correct. Select Repair option Select CMD CD into recovery Type Dir Run the StartRep.exe command in the list.
That should do a basic repair to the OS.