It's kind of a shot in the dark but....
On one PC, a K6 I believe, I kept getting corrupted files. installing Windows fixed the problem but the corruption would reappear about a year later. If you read Windows magazines from that era, you'll see that this was a super common solution to a myriad of Windows problems.
I eventually got fed up and installed Linux on the K6 and the problem became somewhat self-correcting with the Linux FS. That PC is gone now but I got a hold of a P4 years later with the same problem. Pulled it apart to clean it and discovered bad caps all over the motherboard. I didn't know about the bad caps back when I had the K6 so I never thought to check for it then.
I pulled the drive from the P4 and use it with a Linux computer as a buffer now without any problems.
My point? Check the motherboard for bad caps. Look for any that are bulging, deformed, or busted open. If you find any toss the board and get yourself a replacement.
Think your PC is having file problems so the probable cause is the HD going wonky. The file size of the neogeo bios should not have increased so probably a bad file.
Definitely possible. I can't recall the utility that helps check for flakey drives. MS's Disk utility might help but IIRC, it's rather basic. Is it a SMART dive? If its enabled you can check the logs to check the stats on the drive.