Check the PSU and the capacitors on the boards!

Arctic wrote:

Check the PSU and the capacitors on the boards!

I am certain this is not PSU/capacitor related.
But I checked anyway, they are fine.

Check to see if LBA mode is enabled in bios.

kanecvr wrote:

Check to see if LBA mode is enabled in bios.

I was thinking it may be something with his harddrive, considering it happened after an ingame mission. Often it will write some savegame to the harddrive.

ElementalChaos, have you tried using another (known good working) harddrive? I think it is important to rule out any problem that may result in more damage, but you already ruled out bad PSU.

ElementalChaos wrote:

Scandisk found errors in the media descriptor byte and FAT which were repaired, but it didn't work. […]
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Scandisk found errors in the media descriptor byte and FAT which were repaired, but it didn't work.

FDISK /MBR didn't work.
A full surface scan with Scandisk and MHDD reported zero errors.
I tried rebuilding the boot sector with Testdisk. Still nothing.
FDISK reports the partition as active.

I've had these exact symptoms but under different circumstances. When I was testing Clonezilla with a clean install of Win98, this would happen when I'd restore the image. What ended up needing to happen was I had to manually undo the -r flag (resizing partition table) even though I was restoring to the same hard drive that the image was taken from. For some reason this messes up Win98 (I don't have to turn this flag off with any other OS). That said, I could never figure out how to fix the issue once the image was restored. I know this isn't much help, but I thought you'd at least like to know that someone else has seen these exact symptoms that I quoted above.

Maybe it has something to do with the size of the partition table being reported to the OS being messed up.

Good news, everyone!

SYS C: from a Windows 95B boot disk seems to have fixed it. Now that I remember more stringently, I think my problem was caused by selecting "Boot previous version of MS-DOS" in the F8 boot menu, just because I hadn't tried it before and wanted to see what it did. Turns out it renamed the system files I was using with a .W40 extension and DOS 6.22 was stuck trying to boot Win95, which it couldn't.

I went ahead and deleted the DOS6.22 system files as well as the DOS folder, and it still seems to work.