Except for saving the settings in the editor, I've done the calibration as described. Tried resetting different parameters and re-testing, and it seems the problem lies in the Axe FX after updating the firmware. Did a full MIDI reset in the Axe FX, and it seems to fix the problem. Since I have two identical Mission pedals i tried both of them on different FX blocks, controlling different parameters, and they both give the same values on toe down, but different values for different blocks/parameters.