Problem resolved!
When in doubt...read the manual! I went to Input Controller Walk Through and just followed the steps. I noticed that pitch and roll (stick) was only in the one column on the demo, but on mine it was also on my throttle controller, so I highlighted them and hit "clear" so that only one controller had the command. Same for throttle - I cleared it from the stick column.
If anyone has this "fluttering" issue - that will be because one command is allocated to both controllers.
Thanks and I hope this helps someone else.