I had the exact same problem when initially setting up my system. The cure was to shift around your PCI cards a bit. Here's a rundown on PCI slots and IRQ sharing.
PCI Slot 1 shares an IRQ with AGP slot
PCI Slot 2 & 3 share IRQ with ACPI
PCI Slot 4 & 6 share IRQ with USB
PCI Slot 5 shares an IRQ with Highpoint controller
Try to keep slot 1 empty if at all possible, since you really don't want anything sharing an IRQ with your video card (assuming you have an AGP card, that is).