I'm using the standalone version of MMV. It doesn't save controller assignments with a patch either. I just saves one global set somewhere. So all the patches you ever create will have the same assignments, which is ridiculous. I mentioned this in a topic I started back in March, and am including it in my latest post, Massive MMV2 Bug List. Assignments should save with a patch so you can have different assignments for different patches.
If a global set isn't saved when using Audio Units, I should add that to my bug list which will be sent to Arturia in the future.
This forum, unfortunately seems to be almost dead, and nobody seems to get any questions answered. God forbid that Arturia should read posts and answer questions.
-Elhardt