Have you tried using the inserts? The only thing I can think of is the film is moving during the inversions. Even gentle inversions are going to be mini-tidal waves. Those tanks hold lots of liquid.
I use the Jobo 2509n with the Jobo CPE 2 (one speed - fast) for as many as four sheets of 4x5 without the bat wings or whatever they're called. I use the inner most and outer most tracks. I choose not to do six sheets at a time.
And yes, the emulsion side goes inward, away from the walls.