That can be a problem with this design- With a large pump, it runs great, but with a smaller pump, you can get a bubble formed in the base that reduces skimming efficiency.
One thing I did was to drill a hole in the Beckett chamber so excess air could vent from the top of the tubes, and back in to the Beckett hole. Just a 1/4" hole in the bottom of the injector piece, next to the Beckett so air can go from the down-tube in to the Beckett chamber. That way if too much air collects in the down tube, it can recirculates.
If I was to do this model again, I'd go with 2.5" down tubes. They avoid the air-lockup better, even with a smaller pump.
In the base I'd go back to what I have in the "Monster Beckett" thread, which also avoids the air bubble lockup in the base.
Zeph