Anthony,
Are you sure the smell isn't coming from the vents or wet carpeting? Next time you get the bad odor, wipe down the seats with a dry rag and see if it remains. Make sure nothing else (raincoat, boots, etc) is in the car that could be the cause. If the smell comes from the ventilation system there is a cure for that. How old or clean are the mats? A new set of genuine (non OEM mats seem to make a car smell funny to me) floormats can really help out if stains or odors have taken up permanent or semi-permanent residence. If you are interested fill out a PartsShop inquiry and we will let you know about the mats ASAP.

Hope this helps...Lee