Adding the optional support scripts has fixed the Safari issue I was seeing. Usually the install of Cookie walks me through that; it didn't this time for some reason (I recently reinstalled my computer). I've been taking notes on how I did my reinstall and will add a comment about the support scripts to those notes.

I'm having the same problem with Cookie 5.9.2 on High Sierra 10.13.6.

Cookie only sees Firefox (it does not see Safari), and Cookie does not see any cookies in Firefox. Also, Cookie is not maintaining any cookies for Safari (not surprising since Cookie does not see Safari).

I reset sandbox permissions as suggested above, but that did not help.