If the tank is perfectly horizontal, I don't see through which phenomenon the lower reels would get less agitation than the upper ones. If we except the time the developer takes to invade the tank, and to leave it, for the rest of the process the films should receive identical treatment. This difference should be constant between processes.
Are you sure you properly levelled the tank? I found out that putting the level anywhere on the CPP-2 does not level the tank at all. Also, the lift is a strange animal and the tank does not sit perfectly horizontal on the upper basin, I clearly see that my lift tends to "bounce back", if I want it to touch the upper (red) basin (and be levelled supposing the red basin is levelled) I have to press it with my finger. If you level the Jobo, the tank will end up working slightly "bottom up". I have re-levelled my Jobo and now the machine is not horizontal, but the tank is This levelling work is the more important, the longer the tank is.