The known issues are when joint payments are made and then separate returns are filed.  It's easy to program, "check for payments made with either number."  Hard to program, "check to see if amount claimed on separate return is same as, less than, or more than amount actually paid by both spouses, on one or the other account or jointly."  

Will there be an issue if the government shuts down next week and doesn't open until after next April 15?  Is there a charming way to ask, don't you have anything else to worry about?