I dont think any of your 12V issues can effect your 110V power system. The 12 V is on the fuses and all of you 110V power is controlled by your circuit breakers. Although they are housed in the same box with 12V fuses and breakers, they are totally seperate power sources.
Your power converter only uses 110 volt to power/or convert power to your 12 Volt circuits and charge your battery.
What is odd about your 2nd ac is that your saying that it operates on generator but not your shore power. That leads me to believe that a 110 volt breaker is not thrown or it would not work on either. You have a transfer switch that may not be transferring power through both sides of the 50 amp service when it is in shore mode, but is transferring both side when the relay kicks it over to the generator side, therefore operating those circuits going to the 2nd ac. You might check there next.
On another note, you might check your GFCI reset button for those wall outlets that are not working. It can disable all the outlets on the outside of your rig and in your bathroom without throwing a breaker.
Walter and Janie Rogers
2012 Sundance 277RL
TV 2006 Silverado 2500 6.0