Repair Console in Windows XP Professional doesn’t work.

I built a new PC last fall on a SuperMicro server PDSLE motherboard and a Pentium D dual core CPU. This puts me in the catagory of being my own Tech Support and I’ve encountered a problem I can’t figure out. When the PC was finished I installed a brand new copy of Windows XP Professional SP2 that I paid $290 for at Newegg. Now I need to run the Repair Console to fix a problem but the CD won’t boot in the drive. I’ve changed the BIOS so only the CD-ROM will boot and I get return message “Can’t find NTLR”. (It’s there) “No system disk in drive”. The Windows XP CD will perform a install after the machine boots off the hard drive but that’s not where the Repair Console is. Anyone have a clue?