Line 16 on my 1040 only shows taxes withheld/paid from my W-2 and doesn't reflect the $5.9K withheld from my 1099R. It looks like I'm not getting credit for those taxes already paid.
You can review your entry by doing the following:
While in the Forms mode, if the Form 1099-R does reflect a withholding amount, then chose the Delete Form button, and re-enter the information when you return to the interview section of your return. It may be a temporary glitch in the program.