Well, when I had my first problems with the system, I flashed it with the latest BIOS on the SOYO site. I dont' remember the version number, but I'll check that out when I get home too.

By the way, could bad cables attached to more simple things like the CD/DVD drives and floppy drives cause problems? Maybe all my cables were bad...

Also, the OS installed drivers for a lot of the hardware. If I installed the drivers that came with that hardware, could that make a difference?

For example, the items on the fancy cables are:
Toshiba DVD drive
HP SCSI CDRW (on 50 pin SCSI cable)
ZIP drive
Floppy

The items that I did not install drivers for myself:
DVD drive
CDRW
SCSI card for CDRW
ZIP drive

As suggested, I'll also try disconnecting all these drives and pray it's a problem with them and nothing else.