Hello psallo,
Hauptwerk does currently (v4-v6) save/restore the state of the transposer automatically (on a per-organ basis) whenever stopping/starting MIDI. There isn't a means to disable that behaviour, I'm afraid, but we do have an enhancement request logged for potentially adding a preference to do so. I've added your notes to that enhancement request.
In the meantime, if in doubt, I'd recommend making sure that you press your 'TR 0' piston as a matter of course whenever loading an organ. (You can also display the state of the transposer on MIDI LCD panels.)