I have the same tank. How high do you run the water level? Right now I have mine just below the upper baffles. That level still leaves the return lines slightly above the water line. I think it causes microbubbles with those exposed to air. They'll seal up after a week or two but if I adjust them they start right back up.
Here's my equipment list.
IM Fusion 40
Tunze 9004 Skimmer
MP10ESw
Hydra 52
BRS carbon reactor sitting next to tank fed from MJ1200
3 BRS Dosers for Calc, Alk, and top off.
RKE controlling everything
Here's my build thread I need to update.
http://www.reefcentral.com/forums/sh....php?t=2420078