Their are many possible causes, I will outline them in order of probability-
1) Strong flow by the skimmer, especially under it. If their is an undertow from a return pump or powerhead aimed under it this will suck the bubbles down from the skimmer.
2) Skimmer not submerged to the correct depth, if it is too deep or shallow their will be a lot more bubbles. The optimal is about 5.5-6" submerged.
3) Use of additives which contain surfactants (stress coat, dechlorinator, amino acid and vitamin supplements and medications)
4) Saturated Oxygen levels, this one is fairly obvious as the bubbles will get worse the longer the lights are on.
5) Try the pump installed so the intake faces the flow deflector, this will produce the least bubbles in any case.