I'm guessing that at some time you connected an actual pedal and the unit autocalibrated to it. Now it is (wrongly) using the same settings. If this is so, it is a bug, but can probably be fixed by reinitializing the unit.
I believe if you just toggle the "Pedal Calibration Disabled" function from on to off and then to on again that it will delete your current expression pedal mapping. The system property I'm referring to — "Pedal Calibration Disabled" — is under General Settings in H9 Control's Pedal settings screen. It might be named slightly differently on the H9 itself.