Weird thing happened to me last week. After running WinXP successfully from a RAID setup on a PCI card for a few weeks, it suddenly started having problems with other hard drives, and then wouldn't boot XP any more. I noticed one day as the computer sat telling me that it wouldn't boot that the list of IRQs set by the BIOS included three devices using IRQ11, including my RAID card. I pulled the card out and booted from an IDE drive, and everything worked again. Well, everything that was still connected (sniff, no more RAID).
Check your BIOS for shared IRQs; you may have to set some manually.