Badrobot,
I'm not ready to dive in as deep as you are swimming. Your rig is pretty fancy...even if it is white.
As is too often the case, I was wrong about the boot menu being limited to only 4 drives. That is because I thought the reason that one of my WDC 1TB drives didn't show was because of the SATA slot that I had it connected to. I was more alarmed when I tried switching cables, that the Seagate no longer appeared either, and the BIOS run would hang a significant amount while trying to detect drives. I thought that I must have lost both of them, but wasn't ready to accept that two drives would fail simutaneously. After confirming that the Seagate was dead, I also tested the WDC drive in the docking station on the other computer, and it ran okay.
After yanking the Seagate, the WDC now works in the desktop. I have no idea of why one would effect the other, but it did. Sometimes it seems that all that I have to do is to look crossed-eyed at a drive and it will keel over dead. It's ironic that the oldest drive I have that is still working is a Maxtor almost 9 years old. I would still try to buy Maxtors, except that since Seagate bought them out, I don't trust them any longer either.
The bottom line is that the boot menu is now seeing 6 drives, including the 2 external ones, plus one of my optical drives. Still haven't tried the USB docked drive yet, but if that also works, I'll be set for a while, Because I now have one empty drive bay to fill, and I'm not certain when that will happen.