Was the inside of the Aqua Medic bubble counting chamber wet near the top when you put it back in? That could be it.
I was having a problem with the bubbles going up between the narrow space between the tube and the wall of the chamber instead of up the middle where I could see them more easily. I just cut a thin slice of airline tubing, cut it diagonally across the bottom, put it on the end of the inlet tube, and turned the long side close to the plastic. Problem solved. If only I could stop the heavy evaporation.
What's that stuff people use? Glycerin?