You don't say what flavor of Windows you're using, but I used to see that kinda weird stuff a lot in Win95. As I recall, it had something to do with the System Device drivers that were loading for the hard drives.
Goto your Device Manager & expand the entry for (Hard/Fixed/Disk Drives). Right Click on each entry, then select Properties.
If you find one that has 'Compatibility Mode' anywhere on the Property Sheet, that's most likely your problem. What sometimes happened was that Win95 loaded BOTH the Windows (32-bit) driver AND the Compatibility Mode (DOS-sorta) driver for the hard disk, and they'd have a running argument over which driver was gonna use the drive.
The collateral damage was that the OS couldn't arbitrate well enough to ever completely update the Registry entries for the drive, which in turn led to bogus behavior.
Let us know...
~MetaPhysics Applied While You Wait~