Kevin,
If there is 12v at the controller, the mini-breaker in the rear run box is OK. You may not see any voltage at the switches since all three pins are connected to the controller. Since both trays stopped working they are probably sharing something. I'd suspect possibly a faulty ground connection. The diagram shows an 8 awg white wire running to gnd from the controller. Check to see if it is intact and making a good connection to both controllers. You may also want to check the limit switches and verify that they open when the tray is moved (they should normally be closed, providing a gnd signal). Also, operate the switches and see what voltage you see on switch contacts.
Steve