I just set up a 29 Bio Cube and have some bubbles on the surface of the glass, but not coming out of the pump outlet. However, I am not using the stock wet/dry filration in the back, so that might make a difference.
I (literally) just put in some LS, LR, a skimmer and a heater, so I'll let you know if something comes up in the next few hours/days.
are they actually coming out of your pump? how high is the water level in the sump?