I finally found the lock out problem after a week of remote troubleshooting. A Solid State relay "coil" connected to one of the PLC outputs was shorted. I thought I was clever putting in a 1 amp power supply so that all the circuits were protected, but what happened is that the low voltage from the short killed the PLC and left it in a bad state. No wonder it was not communicating! I couldn't forensic it because the PLC wasn't talking every time it tried to turn that output on!
So another moral:
Put a power supply in that is hefty enough to open a separate fuse on the output circuits without dropping the voltage so much that the PLC goes down. Even better, annunciate the fuse so you know what the problem is.