Rather than causing the problem the humidifier may be providing enough moisture for something to live on contamination in the ducts supplying the vents. I would do my best to clean them. Try full strength bleach on a cloth. Reach as far down the duct as you can. If you have access to the ducts, perhaps take them apart, inspect them, and clean each section the best you can. Wearing rubber gloves will be easier on your hands. You could also call in a professional duct cleaning service. Not sure if they would be what you need. I think they are more into dust removal.