Check if the corners of the cover are sitting on the spa. Push down on them slightly. They shouldn't move. Then check the center of the side where the puddle is. If the corners aren't sitting on the spa, but the center is, I'm betting the foam is warped. YES! The foam can warp. Steam is used in the manufacturing process of the foam, and if it's not dried properly during the manufacturing process, the foam can warp shortly after it's sliced off the larger block of foam. Typically the warping can be unnoticeable, except for the puddling like you have.
Unfortunately, I know from experience, that the manufacturer from where I believe the foam came from, has had, in the past, problems with properly drying their foam.
Flipping the cores might solve the puddling problem, but then the center of the cover wont be sitting on the spa. This "gap" allows for a bit more heat to escape. Oh, and if the foam is warped, there's no way to un-warp it.
