I found that the pinout on the EPoX USB3 header is a little different than I was expecting (Pin 10 has +5V power, not ground), so if you have any front-USB wiring from, say, an Antec case plugged into the mobo USB3 header, make sure to leave Pin 10 unoccupied.
BTW, you can update BIOS by putting the new BIOS's .bin file on floppy and Alt+F2'ing at the POST screen if you need to.
The board has been known to act strange with low-RPM or variable-RPM fans plugged into the 3-pin headers. Might want to power any such fans straight from the PSU.
If you have any doubts about the integrity of your IDE cables, see if you have any others you can try. I had some hangups with an A7N8X-Deluxe install... DVD-ROM/CD-RW drive was constantly having errors. Replacing the IDE cable resulted in a 100% cure. Speaking of IDE cables, you want the drive at the end connector so there's no vacant section of cable beyond it (prevents signal bounce).
It's also possible that either your RAM or HDD have errors. If you want to check that, Maxtor PowerMax and Memtest86 might have some light to shed. One of the first people to have problems with an A7N8X-Deluxe turned out to have a faulty hard drive, maybe your drive got rough handling or something.
Or it may be a bad motherboard, of course. Mine is a lot like yours, TruePower 430, 1700+ Palomino and Crucial PC2100, and I did a full Win2000 install with the BIOS settings at Optimal/default settings except I think I switched my printer port to ECP + EPP right off the bat. Good luck with the troubleshooting or RMA.