You didn't mention the type of filtration you use, skimmer, canister wet-dry etc. Do the bubbles apear along with algae or are they just bubbles. If it's algae it could be cyanobacteria(slime algae) or dinoflagellates. Regardless of which, they usually point to a problem with excess nutrients and or poor circulation. If you think your ok on circulation try removing as much as you can and see how much comes back. In my case the excess nutrients came from using tap water instead of RO
to top off with.
Sounds like come really nice rock, please keep us posted as to your progress.