One thing that I have done since I last used CalibreSpy was to move the calibre configuration folder and change the CALIBRE_CONFIG_DIRECTORY environment variable accordingly. Your response seems to suggest that the plugin is storing the configuration location somewhere - it ought not do that, nothing else does -- he says hopefully
BTW: Calibre Spy has always been in my context menu, along with everything else, I prefer to avoid clicking on buttons.
I think it might have had the label "CS+", now its "CalibreSpy", which I much prefer. There's no case for abbreviating GUI plugin names when they're in a context menu, same goes for JobSpy.
BR