Is it working ok under os/2 ? What id do is check that everything is snapped in properly like ram, vid card, etc... Heres a question you mention having a dual boot so 2 hd in case + cdrom + vid + sound maybe a power supply problem. Had one blow up on me a couple of months ago, showing the same symptoms before it went, when I added another cd and hd. Just guessing really tho.
Another thought... have you looked at the mobo when you set up the pc. Heard about peoples capacitors leaking and "bulgeing".