Just went through something similar. Ended up looking at the worksheets in the "forms" section and was able to manually check the box to itemize deductions- I'm married filing separately and my husband itemizes, so that's the box I checked. Do NOT go back to re-run the checker, from that point just move on to the State taxes. I was able to file federal electronically as long as I didn't go all the way back to have the auto-checker "do it's magic". bleh. A real pain in the butt.
