If you have the Duo-therm 4 or 5 button thermostat, the actual control is in a board in your A/C unit. Connections use a 4 wire phone cable, and there needs to be a board for each zone. If you have three zones and two A/C's, there will be a third board hidden somewhere. Mine is over the table behind the Generator/Aquahot/water pump/Fill valve switches, but accessed by removing the vertical dividers inside the overhead cabinets.
If the A/C replacement was done by a tech inexperienced in better motorhomes, they may have connected the cable wrong. If you look online for the Duotherm thermostat manual, it has a good description of the wiring and which wire goes where. IIRC one board is master and the wiring is different for masters and slaves. Access to the wiring is through the return plenum in your ceiling.