I had the same problem. Thinking, OK I can fix this, I jumped in. I changed the thermostat, control board on the front A/C, (zone 1), changed the control wiring , which required me to buy the special tool to put RJ-11 end connectors on new wiring, and I even ran new wiring from the front A/C thru the ductwork to the thermostat located in the middle of the coach. I did learn that the control wiring goes from the thermostat to the left RJ-11 connector on the front A/C control board. The control cable then goes from the right bottom connector on the front A/C control board to the back A/C control board. Also the dip switches on the front A/C are all off, (left position) and the dip switches on the back A/C have the second dip switch turned on. I also found out that only the front A/C has a 12 volt DC feed. The back A/C gets its 12 volt control voltage from the control cable that comes from the front A/C board.
After doing all this I still did not have a working system. I bit the bullet and called around for pricing to replace everything. I have Duo Therm penguin A/Cs with heat pumps. They are both model 630515.321. The best price I found was $975 each plus tax and installation was 4 hours at $120.
I also discovered that the newer replacement model requires a digital programable thermostat instead of the 5 button comfort control thermostat of the old system. I had to buy a new thermostat for about $130. Bottom line is about $2,800 later I have replaced the entire system and it works great. Sorry for the rambling post but I thought someone might use the information.
After telling you all this I would place money on your problem being the front control board that send 12 volts to the rear A/C unit and control signals from the thermostat.
I would gladly give you the new control board I just replaced, However I had the dealer put the old A/C units in the boxes from the new units and gave them to two campers here that needed A/C units. They were both still functional when operated alone as single units wired directly to thermostats.