Do talk to your Scoutmaster now. Ask your advancement chair to get a copy of your advancement record from the council to check for discrepencies. There is little time for errors.
As far as requiring the application to be turned in by your 18th birthday I know of no councils that require this. There are six requirements on the application. Requiring a Scout to turn in an application by their 18th birthday amounts to a seventh requirement - something a council is not authorized to do. Do check with your Scoutmaster, however, as this is something you do not want to argue over.