OK, this is a long one with a multitude of possibilities. Do you know where the bubbles are coming from? Are they in the output water or around the connection of the pump to the cylinder? Try turning off the skimmer for a few minutes, then restarting it. You can get an airlock in it.
Then try adjusting your flow volume and air/water mix to decrease the bubble volume. You can backwash your skimmer by sucking in a glass of warm ro water through your intake as well. Yes, trillions of small bubbles all over you tank are an irritant toyour fish and corals/inverts, so try to avoid them. Large air bubbles in a column of water such as from an airstone are beneficial. Hope you are able to get your adjustments correct to remove those pesky bubbles!
