I have also had issues with my CO2 scrubber. Putting CW in the intake for the scrubber makes the water disappear completely(nothing coming out of the output), but it still pulls the CO2 out of the air.
After letting it run for over an hour, assuming everything was working OK since it was still pulling the CO2 out, not a single drop of water/contaminated water left the CO2 scrubber.
I can provide a screenshot of my setup if it would be helpful