Dave most of the time micro baubles are caused by a air leak on intake side of the pump I would put more teflon tape on the fitting going into the pump and check the hose clamps and make sure they're real tight.
I don't like the sounds of that particular design for your drain. I would highly suggest that you convert them over to a dursol standpipe system like in this link.
http://www.rl180reef.com/180/pages/standpipe/open.htm