I have an assembly with a few hundred components.  Within that assembly there is a flexible sub-assembly with a few different configurations.  Some mates are suppressed in certain configurations but when the configuration is selected within the main assembly, these mates are no longer suppressed.  When I edit the sub-assembly in the main assembly, the mates become suppressed like they should be, but once i get out of editing the sub-assembly, they go back to unsuppressed, which causes mating errors in the main assembly.

So with the sub-assembly open and active, the mates are suppressed in the configuration, but once its in the main assembly, those mates are no longer suppressed for that configuration.  Is there something I'm missing, or is it just a bug from large assemblies?