Our SSDT project doesn't contain any database triggers. Our target database contains a single database trigger, that is managed by our DBA group, so we don't want to delete it. When we generate a script through Publishing the project, the trigger is disabled and re-enabled like expected. However, when we generate a script through Schema Compare, the "DISABLE TRIGGER ALL ON DATABASE" is in the script, but the trigger is never re-enabled. In both instances, the "Disable and reenable DDL triggers" option is checked.
Using SSDT Oct 2013.