I was just suggesting a forum category just for what not to do with a scrubber, and I could post some of these things there, along with anyone else's failed attempts.
For the CO2, that's a thought. I was thinking about adding some fart valves (air traps and release vents) on the return before it gets to the scrubber to reduce the air, and then supply the scrubber with the air bubblers again. If it works, then I'd say its very likely you are right about that possibility of low CO2 in the return air.
Question: If low CO2 limits the growth, then a typical waterfall style scrubber box that is mostly sealed (not air tight though)... Is a few small gaps in the box enough to move the necessary air (with CO2) through for the algae?