I have been using Solidworks since 2003 and never remembering anything like this,
I have a fully mated Top Level Assembly let say with 1 part 1 sub-assembly (Part A config)
The Sub-Assembly has 2 configurations 1 with Part A the other with Part B both are completely separate files.
I then decide to add a configuration to the Top Level Assembly with a different configuration of and decide to use the Sub-Assembly with Part B, so the why is it I cannot move the Sub-Assembly, via Move with triad or drag, until I suppress the grayed out mates that were attached to Part A, was it me or didn't grayed out mean Suppressed?, these mates are clearly grayed and Part A is no longer visible in the Top Level Assembly yet cannot move until I suppress mates that already grayed out?
We just recently moved from 2016 sp05 to 2018sp02 and both me and my coworker have found this very annoying issue.