Well there is a new option that might be throwing you off and you probably aren’t even aware that it is checked by default out of the box.
In Tools > Options > Hole Wizard / Toolbox there is a new checkbox for a feature called “Make this folder the default search location for Toolbox components”. According to the SolidWorks help file this new feature “is useful when you open models whose toolbox components do not reference your Toolbox folder. If you clear the system option, SolidWorks does not automatically search the Toolbox folder for references to Toolbox components.”
Whether this is the cause of your toolbox problems or not, the frustrating thing for me is that this option is checked by default out of the box. I am not a huge fan of new features being added like this and it is automatically checked without being publicized in some way shape or form. Unless you go through each option when a new release comes out (which I think every CAD Admin should) you probably wouldn’t have seen this or known about it.