I personally think gus is right, I've never had to flip my reactors over or drain them or stuff like that (4 24" reactors, 2 by nilocg and 2 diy). I have fixed it by fixing the problem for me, which was the flow was way down (cleaned the canister filter... the sump return pump has never had an issue). My hydor 350 seems to have a permanently reduced flow, I would never put a reactor on it, I don't know if yours is the same. (The flow is definitely reduced from when I first got it by a significant amount and it seems no matter how much I clean it and brush out all the pipes and everything it never gets near what it was originally.) I've never used the aquatop.
I don't think you have to see bubbles everywhere, maybe you can try moving the diffuser around the tank as well as the filter outflow? Or is it an inline diffuser?