Dometic Penguin 2 stops running after a few minutes

Sounds like the leg for the 2nd AC which is separate from the first AC might be bad at the transfer switch when it goes to shore power..could be leg on cord or leg at switch itself...check transfer switch connections...especially on the shore power side of it..the bus might be burnt on the shore power side. Or, something with the cord itself...since it runs fine on generator, the generator side of the transfer switch is fine and no cord is used, thus either the shore power cord or the transfer switch itself where the 2nd leg comes off of might be bad. I am assuming this is from any 50 amp power source, even a campground...If this is only from your house, and a campground is fine, it's the power from your house.

Need more info. You have a 2003 Newmar. The Penguin 2 came with a 12 button CCC tstat module board. Your RV has a 5 button CCC tstat and the other AC has the 5 button Module board. When you install a Penguin 2 with a 12 button module, you must purchase a 12 to 5 button conversion kit and install it on the Penguin 2. IF that was not done then you will have operational problems. Newmar usually installed Heat Pumps back then(2003). The Older HP's had only lo and hi fan speeds. The Medium speed terminal was used to activate the reversing valve for the HP. The Penguin 2 units now have 3 fan speeds and a separate wire for the reversing valve.
1. They did not install the 12 to 5 button kit as required
2. They did install it but miswired it. Doug

Reread your post. Did Newmar offer and install the Intellitec EMS system your year model? If so, they may have miswired the Penguin 2 EMS control wires since the Unit operates OK on APU but not on shore power.