This is caused by a conflict between the global MIDI channel and the Part 1 MIDI channel. See the help pdf "a guide to using the Supernova II Multitimbrally with a sequencer" (Any references within this help pdf to 8 parts should be read as 6 parts for the Nova II).

http://www.novationmusic.com/support.asp?supportid=16&view=TandT