To get micro bubbles in the main tank you either have to have them intially in the return chamber of the sump or your sucking air somewhere through your return......Don't rely just on the simple fact you don't see any water leakage......Air will mysteriously find it's way in....
Another thing I thought of, sometimes a bubble will get stuck in you system somewhere and will need some time to work it's way out, usually doesn't create micro bubbles but can. Try turning the pump of for a moment and see if any air bubbles come out of the intake.