Thanks for the suggestion. It did indeed fix the problem. I saved the CMOS to BIOS first and then after the brain-dump, restored the CMOS back. Now,although I can shutdown, 1 of the 3 disks on the Intel Raid controller isn't recognized as a member of the array - thus the array is offline.
BIOS says that teh SMART status is not recognized. I don't think that they disk is bad since I checked the Intel Manager before doing any of this and the array status was all good. Any ideas? I really don't want to reload from the 6 TB backup array (thankfully I do have a backup).