Here is a work-around.
Go ahead and enter the 1099-R (I assume that you received a 1099-R with a distribution code of 7, and that the source was a traditional IRA).
Answer that you did "something else with it", and finish the rest of the 1099-R interview.
This will be taxed (don't worry) on your federal return.
Now go to the HSA interview (if you need to, do a Search on hsa and click on the jump-to link (Mac users must find HSA in the Topics List). Say that you have an HSA, then navigate through through the interview until you see a screen titled "Let's enter [name]'s HSA contributions". On the second line where it says, "Any contributions you personally made", enter the amount of the IRA distribution here.
This will cause the HSA contribution to appear on line 2 of the 8889. Now, this won't appear on line 10, but you see that line 12 will be the same in either case, so your return will be monetarily correct.
The net result is that the 1099-R will be added to income on line 4b on the 1040, and that same amount will be subtracted back out from income on line 12 on Schedule 1 (1040).
Last thing, put a note in your tax file explaining what you did as a workaround in case anyone ever asks you about this (not likely).
Does this work for you?
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