The JFB System plugin is incompatible with the RocketTheme/Gantry 5 menu editor.
Login to backend of a Gantry 5 website. In a Gantry 5 theme style, select Menu to access Gantry menu editor. None of the menus show any of the menu items for any menu including the menu containing the default menu item. The menu functions normally on the front end but cannot edit with the Gantry editor. On other menus it says the menu is empty which its not.
Disabling the JFB Connect System plugin restores the menu editing function. I have shown this to RocketTheme and they had the same findings.
I run a few other sites with Rocketheme templates that (of course) use JFBConnect. I haven't seen the issue you mention and I just tested to double check. The site below is using the Gantry 5.4.31 plugin (slightly out of date).
I just checked the Menu selection and Assignments (when in a style) areas. They look normal to me and nothing changes whether the JFBCSystem plugin is enabled or not.
Can you try re-ordering the JFBCSystem and/or Gantry plugins so they go before or after the other? Something is obviously different, but unsure what from a quick investigation. We'll gladly help narrow things down however we can though.