I have no experience with the in-tank diffusers. However, I have the same issue with my Griggs reactor in that I need to empty of water every time I clean the canister filter in order to get everything flowing again. This happens even if I pre-fill the canister with water after cleaning. Unfortunately I do not have the space to invert the reactor as PlantedRich suggested. It is not the worst thing in the world but it is a pain and I have about 2 hours of air bubbles in the tank afterwards.
I've been contemplating building a Cerges reactor for this reason, but the design is no where near as simple/fool-proof as the Griggs reactor.
How is your reactor ran? Canister filter?
It is the worst thing in the world for me hahaha. Once a week wrestling the inflow/outflow lines from behind the tank, under the stand, back through the stand doors, yada yada.