I often have subassemblys within subassemblys.  All my parts and assemblies have more than one configuration, and many have many configurations.  I am lately plagued with subassemblys changing their configuration in my assemblies and throwing off my mates, parts lists and everything, and frankly I'm getting fed up.  Someone please tell me there is an explanation for this.

To be specific it always shows up as a wrong part configuration in an assembly.