Well that was an interesting experiment. I have my System drive in bay 1, ProTools drive bay 2. Media drive bay 3 (keep in mind Media drive is the one that was missing).
I pulled out bay #2 first (ProTools drive)... and restart. System drive and Media drive show up on desktop... huh? I pull out Media drive on #3 and put ProTools drive in bay #3... shows up. Confirms ALL drives are working. I stick everything back in the way they were originally... and they work. Go figure. Needed to be reseated? Whacky that the one that was missing shows up by pulling out the one that was showing...???
I even put in the startup disk and repaired all disc's. Disc Utility said they all appear to be okay.
Anyway... thanks for the suggestion that got things moving in the right direction.