I would lift the skimmer out of the water and run a pipe cleaner through the air intake port just to make sure it is clear. Otherwise, if the skimmer is collecting waste and appears to be running properly there isn't much to do. Can you share a photo of your scrubber?
Have you tried skipping the scrubber and just running a continuous air line from the skimmer straight outside? I know you have already invested into making the scrubber but to eliminate indoor air completely, what is pH if you run the air line straight outside? If you decide to do this we might see a pH change over the next 24 hours.
More importantly...do you trust the APEX probe? Mine was reading low, I recalibrated with 7 and 10 calibration fluid and it jumped by .2 due to the probe drifting.