How are you assigning your keyboards to Hauptwerk to set the MIDI channels? You need to auto-detect your keyboard and when doing this there is no mistake in what MIDI channel the keyboard is sending and what Hauptwerk detects. See page 42 of the Hauptwerk user guide as well as our MIDI connection tutorials at http://www.hauptwerk.com/news/tutorials ... to-detect/. Also make sure you have ticked the MIDI port input under Console MIDI IN, not the Sequencer MIDI IN.
If you want to switch between virtual manuals from a single keyboard then you can follow the instructions in the Hauptwerk user guide starting on page 107 for setting up floating divisions which is what this option is meant for. You shouldn't need to be changing MIDI channels on the fly on your keyboard (although Hauptwerk could be set to accept that but it isn't normal).
Hauptwerk simply uses MIDI note on/off for the input. If your keyboard is reversed or if you are having the translator reverse MIDI notes (low C being on the far right) then that MIDI note must be sending note 36 in order to play the low C key in Hauptwerk. Hauptwerk doesn't have an option to reverse the keyboard in this way so you would need to see how to best make your keyboard notes send the proper MIDI note messages and in the order you want them to to match the standard MIDI protocol.