Well, this is funny:
Apparently the size of bubbles in the actual ocean, which varies depending upon complicated circumstances, seems to in fact have an impact on the ration of saturation of CO2 vs O2. Thus, if something about the scrubber is in fact changing the bubble size somehow, it may be causing bubble sizes that are “pro CO2” while a skimmer without the scrubber creates bubbles that are “pro O2,” which would seem to vent off CO2 better and thus increase pH.
The question might then be how attaching a scrubber might affect bubble size.
Thinking out loud, maybe the mechanism is strangely counter-intuitive. Suppose that this is sort of a Laugher Curve. Bubble size from a protein skimmer might be ideal for oxygen dissolving and CO2 gassing at a specific ratio of CO2 to O2. Increase the CO2 (dirty house air) and the bubble size is pro CO2. Increase the O2 instead, and again the bubble size is pro CO2. With too much CO2 from the source, the exchange is pro CO2, so reduction of CO2 gets to the right exchange for pro O2. However, if the air is already good, increasing the O2 too much kicks the bubble size to a different type of pro CO2. The three little bears theory of protein skimmers and scrubbers?
Those seeing benefits from the scrubber but then negative from the recirculating are tweaking too far.
A possible result set, then:
Really dirty air? Scrubber plus recirculating creates the best bubble size, pro-O2, venting CO2. Scrubber alone, not as good. No scrubber, bad.
Somewhat dirty air? Scrubber is the sweet spot on bubble size. No scrubber is worse, but recirculating is also worse because the bubbles get too small/large from the combined effects.
Clean air? Scrubber messes with the bubble size and hurts pH level. Recirculating compounds and worsens the problem.
Room with too much O2 for some reason? Strangely, dosing a small amount of CO2 into the protein skimmer intake would then ironically increase pH by changing the bubble size.