I've installed quite a few of the TrueCharge2 chargers and only ever had one problem - a sticky fan.
Going through the owner's manual the only indicators of thermal shutdown I can see are when the temp and battery leds flash, meaning battery temp is too high.
Are both of these leds flashing? You would have to have a battery temp sensor for this to be indicated. If they are not both flashing which ones are?
If an AC connection is faulty the charger wouldn't be operating properly with the fridge off either.
What is your battery configuration? How many banks do you have? Is the fridge load on the same bank as the halogen lights?
Living aboard in Victoria Harbour