The pump height isn't really the issue. Here's is what happened to me when I first used the aqualifter for my ATO:
My pump and the outflow from the pump were in the sump. Pump was about the same height as the outflow. It kept siphoning water from my res.
I moved the outflow tube higher, the problem stopped.
Now on my other tank, the pump and outflow are the same height. I don't have the problem of siphoning.
I think the correlation here is that the pump and outflow need to be the same height, or the outflow needs to be higher. Just a guess, but that's my experience with it.
Edit: upon reading what I just typed, it doesn't seem to make sense.
Just keep messing with the heights of the pump until it stops would be my advice.
Also, if you're hooking the pump up to a controller, which outlet are you using. The only experience I have is with the apex, and outlets 4 and 8 are designed to be used with ATO pumps. The outlet may not shut off fully and continue to run. If you're not using a controller, try plugging in something like a fan or lamp to draw power as well.