This problem sounds like a bug to me. I'll submit it to the Native Instruments bug list for action. I wish I could provide better help immediately, but for now I'd just suggest to try running with a single document if possible.
While we would like to think of it as a bug it's not. Any time you switch from 1 song to the other Logic loads the instruments, it is faster if they are the same instruments but still obviously takes way too long.