Although I was not the original poster, I was following this thread back in December, because my Aqua C Remora skimmer is also causing many micro bubbles. After Darin said give it a month, I decided to wait and see what happens.
It has been over a month and I am still full of micro bubbles. It seems the micro bubbles initiate with the skimmer. Then I have 2 maxi jet 1200s that must suck them in and they have a burst of more micro bubbles every minute or so (maybe after they build up in there). The maxi that is further from the skimmer does it less frequently and the one by it does it more.
Any suggestion? They are annoying and make the tank appear less clear. Yesterday we cleaned up the tank a little and moved the Maxi's as far as possible from the skimmer, but it is still happening.
54G AGA Corner Tank
Eheim 2215 Canister Filter (w/ live rock rubble in it)
3 Maxijet 1200 Power Heads
Aqua C Remora Protein Skimmer
Acqua C Remora Pre-Skimmer
75 pounds Live Rock
30" 2x65w Coralife Lunar Aqualights
Turbo Twist UV
2 Percula Clowns, Diamond Golby, Flame Angel, Royal Gramma, Lawnmower Blenny, PPmint shrimp, 3 emerald crabs and a huge cleaning crew (snails and crabs)