Well Iv'e looked at the manual, not really helped at all, I had this set up over a year ago, I'm not sure whats up, have the updates somehow changed the way and what aux swithces can be used. ? is this user error..

You might want to try clearing your H9's system settings as well.  Some people have run into some unusual problems after updating which can be resolved just by clearing your settings.  You do this by turning the H9 off and turning it on again with the right footswitch and the HotKnob button pressed (the button in the upper left hand corner of the H9).  This will clear your settings but won't affect your presets.  After you do this, you'll need to go back and configure things as Nick suggested above.