Yep, seems to be a common problem. I don't care how "mildew" resistant something is if moisture gets in there it is going to get moldy.
I had the same problem with mine this year and so did Steve Kroesen and his is a bit newer than mine if I recall. Best bet is to take it off and wash it down with soap and water on your driveway and let it air dry for several hours.
I had a good amount of mold on mine at the swim platform area and had to do this 2 weeks ago. Ended up letting it air dry for a good 5 hours in the sun.
You could also pull it off, clean it, and then apply some water proofing spray. Water is probably seeping through the cover and then sitting on your sun pad causing the mold to grow.
Do you have "vent covers" installed? If not, I'd take a look at putting some of them in. Will help the cover breath a little bit.
http://www.rochfordsupply.com/product_listing.asp_Q_CatID_E_409_A_SubCatID_E_440_A_ProdID_E_3425
Other than all those suggestions, you can also install a damp rid bag in the boat while it is sitting.