I have had this problem in a Mazda. First you have a leak in the trunk, if you are having a difficult time finding it, most likely the leak is around the outer perimeter of your back lights. Sometimes, there is a plug in the trunk that can let in water when you are driving. If the car has sat for a while, you haven't driven it and it gets wet, then it is probably the lights.
The smell is mildew in the trunk.
Also, I just bought a pre-owned 528i and it had that smell. As part of the deal, the smell had to be gone. I pick the car up tomorrow. The detailing guy and I have been talking a lot together. The AC problem is one he has to deal with a lot. My recommendation is don't nickle and dime a "class" car. Take it in and have your dealer take care of it. He sprayed the "whatever" into it a couple of times, checked the filters, ran the car heater on high a couple of times, completely washed all the rugs etc. There might be a bit of smell left, in which case I will return it to have more of the stuff sprayed in again (part of the contract is the car be rid of the smell).
Your service department will be familiar with this problem and will have had to deal with it a number of times already - a common problem with cars with AC.