Just currious - from my home brew days...
How full were your diy reactors (2 liter bottle?)
How large is your bubble counter?
A lot of time, especially at the begging of a batch, bubbles from the beer would foam, fill up the reactor and go into the airlock. In worse case situations it would blow the water out of the airlock, or even blow off the airlock (if it clogged).
In our case the "airlock" is either your bubble counter or your tank. Two quick fixes were to not fill the carboy as much (your reactor), so the foam would not reach the top, or use a larger airlock (bubble counter) to catch the foam. My personal favorite (for beer) was to use a larger hose (foam would not travel up a 1" hose) - but not sure how that applies to aquariums yet.
58 gallon oceanic, Kessel 360 tun sun, pressurized co2, eheim pimp #179 - 2217 and diffuser