"The issue is the 1099R reflects on line 2a the withdrawal amount (even though repaid in 60 days) for both the withdrawal and RMD."
That's correct reporting on the Form 1099-R and the Form 1099-R must be entered as received.
In the questions that follow entering this Form 1099-R, did you indicate that part was RMD, indicate that $16,504.19 was RMD, indicate that you moved the money to another retirement account (or returned it to the same account), indicated that you rolled over part equaling $45,000 and cashed out part? I suspect that you did not correctly indicate the rollover of the $45,000.
