I have Windows on my Raptor, but PC will only boot to Windows if I change the hard disk priority in BIOS so that the Maxtor is first. This is then set as C: in Windows, with the Raptor set as D. If I don't set this, or I unplug the Maxtor completely, I get "Disk boot error" (or something similar). I've tried changing around which SATA ports go to which disk, but nothing changes. I don't think that's the issue anyway as it did it on other mobo's. I'd like to get rid of the Maxtor as I've just ordered 2 1TB drives but I can't if my PC won't boot.
More recently I've developed another boot issue...
Sometimes when I try to load Windows I keep getting the "missing or corrupt hal.dll", and the only way Windows will boot is if I set the 1st boot device as CD-ROM, and have the Windows disc in the drive, let it spin up but then don't press anything so it goes on to boot from the hard disk.
As for the Hal.dll issue, begin like you are going to re-format and re-install windows. When it gets to the area to ask to format the drive, there should also be an option to run repair on the windows installation. Do so, and this should fix your hal.dll problem (had similar issues with MS Server, and XP)