After booting sans mouse, dump out /proc/interrupts and see what else in the box is using IRQ6. Of course, if the BIOS is shuffling things around from boot to boot, that may not prove anything. Does the boot log on failure show any other IRQ6 devices?

EDIT: Oh wait.. IRQ6 is usually reserved (exclusively) for the floppy controller. I doubt that it can be shared safely.

Any way to force your BIOS to use a particular interrupt for the 3ware slot? Most AWARD bios systems can do this, as can some others.

Cheers