You can try moving around some of your PCI cards or hard assigning them IRQ's. The IDE Bus sharing an IRQ with PCI devices can give your system fits, even if there aren't any IRQ conflicts. Try using the lower numbered PCI slots (1,2,3) first as they have priority over Interrupt Requests.
I moved some cards around when I reinstalled my Lite-On 24x burner..was running fine at 150mhz FSB, but after the swapping and install, and Windows wouldn't finish loading at any speeds higher than default! Moved the PCI cards back to their normal places and I'm back raging along at 150mhz FSB.
Chiz