Previously I had each F2 connected to its own sub out on the Marantz (and prior to the Marantz to an Onkyo 5507). So the volume was always in balance. Now with my current hook up, I have a feeling that for every 1db increase on the volume dial, I am getting a 1.5db increase in actual volume. The first F2 and Paradigm are adjusted properly but because of the loop out to the second F2 I am adding extra output that the Marantz is not aware off. At least, that is what I am thinking. I hope I am wrong. It is basically correct at one volume setting, the one at which it was calibrated.
Were all 3 subs connected and powered the last time you ran the calibration? If so, it will all work correctly as you change the volume. There's no way it couldn't. Even if they weren't all connected you'd have a constant offset across all volumes.
Are you sure you're not noticing the affect of some sort of Dynamic EQ?