As I mentioned I added a new controller card to my server. Before hand it had an Adaptec 2940U2W (which replaced the onboard 39160 which failed and I miss) and a Promise Ultra133TX2. I had the SCSI card as primary boot and the EIDE card as secondary. After I added the High Point RocketRAID 1520 it off course added itself as the primary boot device in the BIOS. I went in and moved up the SCSI to the top and also disabled the EIDE and SATA cards from possible boot. At this point the machine wouldn't boot at all. I tried lots of stuff and then I eventually went back in and set the other cards to later in the boot order. Then it worked again.
It seems the cards need to be in the boot order for their onboard BIOS to load properly. At least with my Supermicro P3TDE6 motherboard. This was an oddity I had never encountered before.