I have exact same problem and have been banging my head against the wall trying to get it to be consistent. I was about to abandon the bh-1000 for a remora, when I just realized there is a pretty stupid design flaw with the unit.
The plastic ring that secures the airline tube to the skimmer body is in a pretty stupid place. It routes the air tube up behind the tank and pinches it between the skimmer body and the glass. I even had the leveling screws loosened pretty far out and it was still pinching the tube.
I'm guessing the restricted air flow would be enough to cause the water level to rise just high enough to be totally annoying. Add the sensitivity to water level in the main display, and it just makes it worse. Restricted air flow would make the water level higher, and make it skim more wet. The wetter it skims, the lower the water level in the tank gets.
I took the airline tube out of that ring, and am just letting it hang behind the tank while I see if it makes a difference.
That ring that secures the tube should have been on the side or back of the unit. Not between the skimmer and the tank glass where it gets pinched.
I don't know if this is the solution. I wrote to customer support to complain about same issue, and am waiting to hear back on Monday.
Hope that helps.