These are a couple articles I found online describing your situation. If you've seen them already ... sorry. If not ... hope this may help.
Brian
1)
Why does my SeaClone™ protein skimmer periodically put so many fine bubbles into the tank?
During the first few days of operation the skimmer has a tendency to put a small amount of bubbles into the tank; this is normal and the bubbles should dissipate during the skimmer's break-in period (2-4 days). It has also been observed on many occasions that the addition of products which claim to promote a thickened slime coating on fish tends to make the skimmers put bubbles into the aquarium for a wek or so. This problem usually dissipates over the course of one or two weeks.
If bubbles persist, however, it is usually an indication of too much water flow and not enough airflow. You can check this by looking at the depth of submersion of the venturi air intake (located at the Maxi-Jet™ pump intake). The venturi should be 2 to 2.5 inches below the water surface. Often, the venturi ends up about 4 inches below the surface so it may be necessary to cut off a short length of the "J" tube to raise the pump to the appropriate level. Raising the pump closer to the water surface will increase the airflow and decrease the water flow.
Once the pump is set at the proper level remove the cap from the air intake adjustment bulb. This will be the setting which allows for maximum air flow and minimum water flow; there should be no bubbles going into the tank at this setting.
AND FROM ANOTHER SITE
2)
Problem: Skimmer is spilling large amounts of fine air bubbles into tank and/or the collection cup is rapidly filling with water
Possible causes:
A "slime producing" additive has recently been added to the water. These additives, often used for their de-chlorinating or ammonia neutralizing capabilities, contain thick gel-like agents that are not compatible with the vigorous air/water mixing that occurs in a venturi style skimmer. The only recommended action is to unplug the skimmer or to close or remove the air intake system until it has been at least one week since the additive has been used. The slime-producing agent will eventually break down and skimming action will return to normal. Some brands will take as long as 3 weeks depending on the amount of additive used. Simple de-chlorinators and ammonia neutralizers should not cause a problem. Only the products that claim to thicken a fish’s slime coating will produce these effects. Remember that protein skimmers remove and react to organic compounds dissolved in the water. Any water additive that has an organic base may affect a skimmer’s production for a short time period.
The pump may be submerged too deeply in the water. The deeper the pump and venturi intake are submerged, the less air will be drawn into the skimmer. Less air will give higher water flow, which will carry bubbles out into the tank. Make sure the venturi intake is submerged by 2 to 3 inches. You may have to cut off a small length from the end of the J-skimmer tube to achieve this.
