Please Help with Hard Drive/Reboot Problem

I'm running XP SP3 on a machine that was built back in May.

Everything was great until Sunday evening.

As I was exiting out of a game that I have been playing for years, the computer rebooted. Not a CTD.

The motherboard (from Gigabyte) has dual BIOS and upon reboot, it reloaded the BIOS.

After poking around, there were a large number of files on the boot drive that couldn't be seen from explorer. Some of these files were in the windows/system32 folder.

I ended up running chkdsk /r and it corrected a number of problems. However, I am still having a problem with random rebooting of the machine.

I think the problem has something to do with indexing of the hard drive. Is there some way to verify that the index is correct or am I stuck reformatting the boot drive and starting over.