I have noticed the same. The File Sync rules seem to get priority over Profiles so if you have a large File Sync (like a LifeGuard update for Zebra devices) you will have to wait for that to process before any of the Profiles get assigned. You may need to institute a Staging group concept if you want to work around this priority. We use this concept to ensure that the OEM specific plugin is installed first before any additional Profiles or File Sync rules are applied.