E-filing of Taxes

I also use Turbo Tax and pay for the update each year, but I mail them in to the IRS. The option to file on line is available, but I don't use it and don't trust it, too many things can go wrong, such as what you describe.
If I were you I would call the IRS 800 number and talk to an attorney, yes, they have plenty of them, just explain to him/her what happened, surely some mix up with the SS #.
Good luck !