My federal return was just accepted after I resubmitted it without modification, so perhaps they have now fixed this.
Timeline:
* Submiited Federal and State returns at ~8pm Eastern on May 4
* Got the 'Duplicate 1099R' email from TurboTax around 9:30pm
* Reviewed my 1099Rs, but did not modify them. Resubmitted the returns at 12:40am May 5
* Got email saying federal return had been accepted at 1:05am
