OK I’m stupid. I was assuming that when you were on for example MIDI Channel 2 that any Flexphraser stuff created from that channel would also be MIDI Channel 2. However the Flexphrase stuff is always set to MIDI channel 1. So you either have to edit the Flexphase and change all notes to the MIDI channel you want or (easier) set each of your tracks to MIDI channel ALL.
Problem now solved. Still think it would be logical for any Flexphrase generation to match the MIDI channel you were recording from.