When I try to save some time by building a finished assembly to insert into another assembly it doesn't behave as it should. 

When I build the first assembly of lets say assembly A, some parts given the mates, will spin relative to one another. When I save assembly A and then drop it into assembly B to mate it, it no longer spins. It may be possible that my options are somehow checked to fix or something but I don't understand how to make an assembly that will function inside another assembly. The parts always go to stiff relations when I drop it in.

I can't share files and I'm not going to create dummy files for this question because it would waste a lot of time.