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.