Are you sure you have the re-directable outputs disabled (set to unused channels) on the 're-directable MIDI inputs' tab of the settings screens?
It sounds like you are somehow getting MIDI note-off messages routed to both the manual and pedalboard. Or is your MIDI hardware sending MIDI 'all notes off' or reset messages when it shouldn't? To my knowledge there are no bugs in Hauptwerk's implmentation of borrowing, i.e. if you play a pipe from two keyboards and then release the note on one it will keep sounding.
I would recommend running MIDI-OX when Hauptwerk isn't running to check the MIDI messages that are being received by the computer:
http://www.midiox.com/
Martin.