I found some useful information on wikipedia. It agrees with MaransGuy and says that mold in the winter forms because of drafts, and mold is a problem in warm months when it's too air tight.
Our pullets weren't going in the coop at night, prefering to sleep in their run. I didn't want this habit to develop so I had been putting them in and closing their hatch at night several times last week. That would definately have cut down the air flow, and now we're paying for it. I bet we're on to somthing.
From wikipedia: If there are mold problems in a house only during certain times of the year, then it is probably either too air-tight, or too drafty. Mold problems occur in airtight homes more frequently in the warmer months (when humidity reaches high levels inside the house, and moisture is trapped), and occur in drafty homes more frequently in the colder months (when warm air escapes from the living area into unconditioned space, and condenses). If a house is artificially humidified during the winter, this can create conditions favorable to mold. Moving air may prevent mold from growing since it has the same desiccating effect as lowering humidity. Keeping indoor air temperature higher than 74 °F (23.3 °C) also has an inhibiting effect on mold growth.