I had the same problem. I was rejected three times even after checking and double checking the name, spelling, payer's ID, etc. Then I deleted all the 1099-R's I had hand entered and downloaded all of them directly from the financial institutions. On doing that I noticed that one 1099-R had a different address for the payer on what was downloaded compared to the paper 1099-R I had hand entered. That was the only difference I could find. I then re-efiled and IRS accepted it immediately.
The payer 1099-R that was different was for a Fidelity IRA account.
Lesson learned: download stuff instead of hand entering it whenever possible.
