I currently have a coralife 29 gallon biocube. I also had the same problems with micro-bubble that you have. I run a aqualife 115 skimmer in chamber 1, use stevet's media basket and fuge in chamber 2. CHamber 3 has the return pump and heater in it. The bubbles were not coming from the skimmer as I had originally figured. Never did figure out the cause but to fix it I put my return pump in a filtersock and keep the back chambers filled to the first lip in the back chambers. Problem solved. Good luck with resolving yours!