I have a similar issue. However, both of the 1099Rs are for my wife. One is from her Traditional IPA and the other is from her Roth IRA. Different amounts, different account #s, different distribution codes and the Traditional one has IRA/SEP/SIMPLE checked. But they both are for my wife from the same payor. I've reviewed both 1099R entries and made sure everything is correct for each. I still get rejected as having duplicate 1099Rs. I'm not sure what to do now.
