Dragging this pre-extension thread back to life. I went to prepare a return tonight and it was showing the 1040 as accepted (with no extension). 

Turns out by filing the client's ex wife's return in March, the program showed his efile status as accepted. We use the EF Status for filing extensions so no extension was filed. Should be fun to explain to the client and to the IRS when trying to get the penalties abated (he owes $20k).

Found two other clients with the same issue. Luckily they both get refunds.