i have done the same. went back to push with manifold and pull thru masterflex for almost a week now without any issues. i used this method for 3 months without any issues before changing to just the masterflex. i believe the issue is when there are no pressure the recirculating pump is somehow drawing air back.
Yeah I would say that pulling is definitely better than pushing when using a peristaltic pump. Absolutely no issues with bubbles in the CaRx chamber. Now tuning it again. I think this will also making tuning easier by pulling exactly the amount I want.