Well, I've run 2+2 configuration for years now. I know it works. Depending on which 3.5 drive is first in the chain though, it could be you blew something on the pass through board.

I've seen that exactly once though and it was when I plugged an AE 3.5" pass through board upside down by accident, then after that no matter what I chained to it, there was no more chain.... Albeit I doubt you opened your drive case and fiddled with it yet right?

If you are using the standard 800K Apple 3.5" drives you should be fine with the standard Apple 5.25" Unidisk or or Unidisk Platinum drives daisy chained with them.

Not sure what else.