So basically what I have happening is that when I go to save an assembly containing Smart Fasteners or other toolbox components, it attempts to save the configurations in the assembly as individual part files in the same directory as the assembly as though the Smart Fastener/Toolbox Component was a virtual part.
Is this an option somewhere? I've never seen it attempt to save smart fasteners before.

I have also noticed that the Fasteners will loaded wrong when opening the assembly. They load the "Cfg-preview" and display that. A simple editing of the part reverts them back to the named configuration. Possibly related?