When editing a Toneprint in the PC/MAC editor please ensure you are checking the mapping section before saving your edit.

If the settings show as pictures in the screenshot below it will mimic the settings on the physical pedal, when you save the Toneprint this will revert to what is set on the knobs of the pedal.

To save a Toneprint without it doing this please change your settings in the Mapping section to the following, once saved your edited parameters should be the same.