Did a re-install solve your issue?
If not.
On what MIDI CC does your Sustain pedal transmit?
the sustain pedal works fine if I close Piano V2 and use the KeyLab88 to control an off-board module.
it is set on Sustain and inverted (as it should be for this pedal to work correctly).
You mean a hardware unit?
Please keep in mind, that different hardware units may require different Sustain Pedal polarity settings to work correct.
Be sure the polarity setting work for Piano V2.
But anyway - this don't explain the transpose behavior you mention.
I also checked the Sustain Pedal settings in EDIT mode
You mean MIDI learn button activated?
according to the board
Please explain what "board" is or perhaps post a screenshot of this.
A screenshot of the Global Tension Transpose MIDI Learn settings might help.