Wifey B: Don't believe in winter.
We keep our RIB's in normal position and covered. I was wondering why people were talking sun damage and not using cover. However, now see dougcole's post.
We're not having the problem as you describe even on the one we have on the swim platform. Materials are important and I do know natural materials are lousy for mildew and polyesters and acrylics much better. I know Stamoid is a vinyl coated polyester and claims to be mildew resistant but don't know. Here's a cool listing of the various fabrics. We use Sunbrella which is an Acrylic.
Best Boat Cover Material Discussion!
Now something you may not have although the Stamoid people have them on their site. That's a boat vent. Here's the Boat Vent II
Sailrite - Fabric, Canvas, and Sewing Machines Since 1969
They have a sewable one too.
Sailrite - Fabric, Canvas, and Sewing Machines Since 1969
I know a lot of people don't have poles under their dinghy cover. These require poles. If you don't have the vents, I'd talk to Sailrite about it.