They should have different box 7 codes.
One should be coded "2" (I think...was for me when I reached 59.5)
The other should be coded "7"
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IF that doesn't work...then the software folks are trying to prevent people from double-entering 1099-R forms, and if the $$ are exactly the same, they kick it out as a duplicate.
IF that is the case here, try increasing boxes 1 and 2a by $1 on one, and drop boxes 1 & 2a by $1 on the other.