Nik, the association engine is actually the same engine that is used for league, champions league and cup matches.
What's happening is that their is a cultural component to tactics. Basically, some nations, especially those with a rich footballing history have a cultural signature to their play style, whether it be a counter attacking style, tiki-taka, all-out attack, etc... Since several servers are heavy with one or two nations making up the vast majority of the managers, managers tactics and they way the game is learned is being defined by what the dominant playstyle(s) of that server are. So the tactics that work best on one server, won't necessarily experience as much success on a different server. What's happening with association is that the servers are being merged together, so managers on server 17 and playing against managers on servers other than server 17.
Here is my performance in my current association
27 total bonuses given so far; haven't missed bonus. 27*6 = 162 maximum points. I've earned 147 total, for 147/162 overall. An overall record of 48-3-3 since I joined this association. I don't believe that pace to be sustainable, but over my last 54 non association matches, I have the same exact record of 48-3-3.
Basically, association, league, cup, CL/SL all are the same game engine, but footballing culture defines tactics, so managers on different servers are learning the game differently, due to different styles of play.