Its a programming problem they havent been able to fix. 

Once an amended return gets rejected for some weird reason it stops recognizing it as an amended return and you cant resubmit it.  I fought one for weeks last year, I tried every trick I could think of short of redoing the entire return and saving it with a new name (it was just too complex), I finally gave up and mailed it in on paper.

EFiled 1040Xs arent processed any faster than mailed in ones you just save the mailing/sorting time. 

If its a simple return you might want to start over from scratch with a new file name, but if its complex, cut your time losses now and just mail it.