003 Rack I/O's messed up

I was successfully using my DIGI 003 Rack with an ADAT giving me a total of 16 channels when all of the sudden, the next day, my session wouldn't recognize certain channels (I hadn't changed any hardware settings).

I upgraded to PT12 and downloaded the 003 drivers and now I'm not able to assign any tracks to the main outputs either, their just not there for some reason. Any suggestions?

Caleb

MBP 2012 i7
10.10.3
PT 12.1.0