Brad

Feel for ya! Time to learn Simpl. Crestron releases beta system builder software about every 2 weeks, sometimes twice a week. It is made to fit into the box. Sounds like the system you have is too big for the box. About 4 years ago I had a large SB job (Boss wanted SB, I wanted to use Simpl) and it came to a point where it wouldn't assign anymore joins. I maxed it out. I was SOL for about a two weeks untill Crestron released a fix.
Crestron DOES fix their stuff. Sounds like you just happen to be pushing their limits at this point in time and/or found a bug.