Anyway, while down bags aren't ideal for really wet conditions, they can be made to work. You have to keep them as dry as possible in the tent, of course. And when you first get up, unzip the bag most of the way and lay it open so the lining is exposed. That will help speed evaporation of moisture that came off your skin during the night. And if any sun comes out, by all means get the bag into the open for as long as convenient. Don't mess with a campfireyou'll melt holes in the bag.
For a stuff stack, I typically use an Outdoor Research bag made of a waterproof material but without a dry-bag seal on the open end (example: OR's HydroLite #3 Stuff Sack; $12, www.orgear.com). So that's not much different from your zip-type bag; the OR bag doesn't allow the bag to breathe and dry at all. Besides, I use the OR bag for the same reason you use the zip bagto keep the thing dry during the day.
Anyway, for all of that, I'm a little stumped. Try this: Let the bags air out thoroughly in a dry place for several days. Look for small black spots anywhere on the baga sign of mildew. It may be that a few spritzes of an odor-remover such as Febreze will take care of the smell. But, you may have to launder the bags. For that you'll want to go to a Laundromat with commercial front-loading machines. Toss in the bags and a little down-specific soap such as Nikwax Down Wash ($9; www.rei.com). Wash on warm, then run the bags through an extra rinse cycle. Then dry the bags, also on the warm (medium) setting, for as long as it takes. Down bags actually launder pretty well. Store them in a loose, breathable cotton sack. It wouldn't hurt, before storage, to also run the bag through the clothes dryer to ensure it's thoroughly dry.
Hope that helps!