Marc,

It should prove easy enough to determine if you have a leak. Get the inside good and dry, put your spray skirt or cockpit cover on the boat, and run water on the deck. Start off gently at first. If it stays dry, get more aggressive with the water. If the water is not finding its way in via hull fittings, crack, or a pinhole, then the only two suspects left are the spray skirt, or as you guessed, condensation. I don't think I have ever noticed condensation in my woods boats though. The inside deck surface would have to be colder than the surrounding humud air, and that does not seem likely in a warm paddling environment. Perhaps your spray skirts is leaking at the front where the water can wick to the underside of the deck.

Ted