Configurations Problems

I have ran into a problem with an assembly configuration i am using.

Here is what is happening.  I have an assembly that has four different configurations. The reason i am packing  and going the assembly is that one part on the assembly is getting swap out with a similar part that has different features on it. Well it packs and gos cleanly and the new part swaps in perfectly. But when i swap this newly created assembly into where the old one as the assembly get mating errors.( faces do not exist) but only after it is swapped into the assembly. Does anyone have an idea on why this would be happening?