Been there, done that and even bought a T-shirt...
Let me give you a little back ground...I had the same problem except it was with my windows. The fuse would blow, but you could still operate both back windows from the actual doors, just not the center console. I traced the problem back to a part called the "power convenience moduled" This item is a black box located under the rear seat drivers sdie and is big $$$$$ to replace. I ended up getting a used one for $125.00 from a place called PGAUTO.COM
This may be a wild shot or it may hit the nail on the head. See if your local dealership has one and will let you plug it in and see if it works. My car is a 124 series and the new part has a part number that begins with a 202 as opposed to a 124.
What is ironic is that the following week after replacing my control box, my friend had the same problem with his sunroof, as you are describing..BINGO it was the box that went bad.
Let us know how it turns out.