Hello @Boozebeard,
I’m not immediately experiencing any issues from your description. Changing the Preferences> Export flip settings has an immediate impact on OBJ on both the current Mac and Windows versions of the program when exported to another application. Please keep in mind that a target application may also have its own preferences governing the import and export of files. Remember also that the configuration must be stored with Preferences> Config> Store Config in order for changes to be remembered at startup.
Otherwise, if what I describe is not your experience, for technical issues with ZBrush please contact Pixologic Support.
Thank you!