If you've saved the presets in the GUI, you still need to write your QubeGUI prefs to disk so that AE can use the updated prefs.
Either File->Exit the QubeGUI gracefully to save your prefs, or explicitly save your prefs with File->SavePrefs.
You shouldn't have to restart AE, it should read the prefs from disk each time it launches a submit UI.
That being said, some versions seem to have had a separate set of prefs for AE internally; you may also need to do a "Preset Set" from the submission UI launched from inside AfterEffects.