I built a system a while ago for someone using the sk939 MSI neo2 platinum board and an A64 cpu, and had many problems getting devices to work.
With everything enabled in the bios, USB wouldn't work. Neither would a couple of the IDE channels, firewire and audio. Device manager in windows...
I had a fuckload of problems with this board, windows couldn't install half the drivers because there were apparently not enough IRQs left for them, i managed to get everything working by disabling a few unused things in the bios.
This was with the latest bios too.