This is a known issue with an easy workaround: Go to the View menu and click ScriptNotes. This will make the ScriptNote markers visible again.
NOTE: Live support for Final Draft 7 has been discontinued. You will still be able to install, activate and use FD7 on appropriate computers but email, chat and telephone support is no longer available. Live activation assistance will be available via phone (818-789-6281) and email and chat (links on the left side of this page) until June 14, 2017.