I have an upgraded seat in my boat. Lately there has been a lot if water in the flap behind the seat. I fold th seat back before covering. Nothing on the boat is wet. It is a mystery!
That's very odd. Maybe you need to spray the cover with some 303 Fabric Guard protectant. I would go that route first. I have never had an issue with my chair and I keep it fully upright.
I agree with azeay2007, just make sure you take the cover off the boat and drape it over your trailer when you spray it as some had problems with staining the seats if it dripped