Angus, I was thinking about your differentials difference in your Synergy vs your Alliance.
Looking at the some pictures of these planes, it seems that there is not a great difference in terms of thrust-wing line. Can you confirm this?
If so, this again proves that thrust line is not the explaination
PS: two pictures of these planes can be found for example here:
http://www.singahobby.com/mkp02.html