In the past when I had volume changes on a bounce to clip melodyne clip is was because either
a) I had the track level set at other than 0db
2) I had FXs enabled that altered the level of the output
Now, I ALWAYS move my clips to a blank new track for melodyning then move them back after I bounce to clip.
Don't know if that will help but it's worth a try.
I can't imagine what the mototboating is but it may be related.