About the only possibility (given the symptoms you have) is the small transfer switch used to power the front air conditioner from either shore power or generator.
It appears that the normally closed contacts on this switch are not making good contact. Take a look at the diagram attached and you will see that the front air conditioner gets it's power through the small TX/switch, from the main breaker, when on shore power, but directly from the generator via the tx/switch when gen is running.
This TX/switch is usually located near the main circuit breaker panel. Possibly near that control unit that you replaced. It may be necessary to remove some paneling or covers to find it. A good sharp rap with small mallet will usually free it up.
The transfer switch shown in the upper left is your normal power transfer switch. The transfer switch being discussed here is the one in the middle of the page. Air Cond. unit #2 is usually the front unit in your rig.
If each of your air units are fed from their own individual circuit breaker, then the problem could possibly be in the path from the breaker to the small TX/SW. Check the tightness of the screws on the breaker feeding that unit. (including the white return wire for that circuit)
