When preferences sync is enabled, Firefox Sync will synchronize preferences between the same application based on a whitelist. That means preferences between Firefox and Fennec, for instance, are never synced. To sync preferences between Firefoxes, Fennecs, Thunderbirds, etc., ensure the prefs are whitelisted.
The whitelist is determined as follows: for each services.sync.prefs.sync.<pref> preference that is set to true, Firefox Sync will sync the <pref> preference. For example, if your add-on had a pref called extension.frobnaz.foobar, to have it synced, create a bool preference called services.sync.prefs.sync.extension.frobnaz.foobar and set it to true. The most convenient place for this would be your add-on's default preferences, though if you want to give the user a choice to opt-in, you can also do it programmatically. See adding_preferences_to_an_extension.