Hello Mark,
If Hauptwerk's transposer had accidentally been turned on then it would affect all of the virtual keyboards equally (not just one), so that can't be the problem.
Also, if you had accidentally adjusted the key-shift setting for one of the virtual keyboards within Hauptwerk then it would only affect that one particular sample set, so that almost certainly isn't the problem.
My guess would be that you have accidentally turned on a transposer function within the MIDI keyboard itself. Is that the case?