musky smell from air conditioner

We had the same issue with our Jayco. It turned out that the water had seeped between the roofing material and the roof deck. What we were smelling was the rotting roof deck. I hope it is not the same as what you have but Jayco fixed the roof under warranty and the smell went away.
One way to check is to walk on the roof and check for soft spots. Ours was towards the back near the ladder.