Can't boot from 2nd SATA controller

I have the MSI K8N Diamond Plus, which has 2 SATA controllers, the Nvidia (4 ports) and the Silicon Image 3132 (2 ports)

I have 2 Raptors in Raid 0 and 2 WD Caviar RE2 WD4000YR in Raid 0.

When I first built the system I couldn't get the Raptors to boot from the SI controller, but they booted fine from the Nvidia. I couldn't figure it out, so I said f'it, I'm ready to install XP and see how fast this puppy is. This was about 6 weeks ago.

Well this weekend I finally got around to adding some extra fans and another hardrive cage to separate the drives. Well I forgot to note which controller was using which drives when I unhooked them, so I guessed, but I guessed wrong, and hooked up the OS drives on the Silicon and the storage drives on the Nvidia.

Well it still wouldn't boot, even after I confiured the bios to boot from the SI controller.

Any ideas? I didn't hurt the array by hooking them up to a different controller did I? I did go to each of the controller's menu and each array detected fine.