Okay, I spent a good amount of time on line with Dell support after rebooting the Library (the 30 minute post was pushing past 3 hours) and they had me try a couple things. It seems like it's going to come down to faulty hardware. The Dell tech had me disconnect the working unit and change the control paths on the non-working ML6000. It has:
0,1
0,2
-1,4
It was set to -1,4 and the Dell tech said it shouldn't matter which one it was on, but each time I changed it NBU would detect it differently. From 1 drive path and no robot, to 2 and no robot, to 1 and 1 robot, to nothing, and back around until we finally landed on 2 and 1 robot. So I hooked the working unit back up and NBU was able to detect 2 robots and 4 drives. Looks like we are good for now but that shouldn't be occuring at all. We will have a Dell tech come out and test the hardware.
Thanks all for your help.