I think you want to make the input to the bubble counter go only about one inch below the water line, then the output line is about 1 inch above the water line. the reasoning is that the pressure in the generator has to push down against the level of water in that bottle, then again inside the tank. So, keeping the input lines low in the counter and in the tank just adds unnecessary head pressure to the generator. Otherwise, the best guess is still leaks, try submerging the system in a bucket of water to see any leaks, after you reduce those input lines if it still doens't work.
PS, also be certain there is not any water in the line going to the fish tank, for the same reason. It doesn't take much water in the lines to add several inches of back pressure to the bottles. For that reason, it is wise to keep your generator and bubble counter on top of the tank until the unit is bubbling into the tank well. At the start, when there is some CO2 in the line but no real pressure or flow rate built up, the CO2 is so easily absorbed that the water will travel up the line. Once it is over the rim of the tank, gravity pulls it down, filling the line. That many inches of water is just too much for the generator to work against. So, inspect the line, and shake any bits of water back toward the tank.