Andrew, a Bak Pak will do this for the first 20 hours or so of operation. Mine did the exact same thing and now its absolutely perfect. if you go to the CPR home page they have a list of FAQ's. it shows that the bubbles are a result of new operation and they will also do the same thing with large doses of chemicals and when you move the stuff in the tank a bunch. You will love this skimmer!

~Dust