Gombo - You have a crack in the cover foam on the control side. Open it up and I think you'll find I'm right.
Puddles that small will not harm the cover, thought they can make water stains. 303 will help minimize the water staining and make it easier to clean them off if they do form.
Mine does that, but it is close to ten years old. It was under a patio cover almost since new - I took it on a trade, have had it in full sun for a couple of years, and will be replacing the cover soon.
If my new cover holds water like the old one, I will be sending it back for a replacement.
8-)