Does your skimmer draw in its water from the surface? The stuff floating atop the water is pollutants, I may be wrong here, but the air-water interface on the top of the tank is sort of like the surface of one huge bubble, that stuff is more or less the same sort of stuff your skimmer is designed to remove with its many tiny bubbles.
If you could figure a way to have your skimmer draw its water in from the surface, the problem would be reduced or eliminated, you could also point a powerhead so some of its flow breaks the water surface, reducing its surface tension quite a bit and getting that stuff in the water column so it can be processed by your skimmer.