I have exactly same problem as you. I have profit in Schedule C, but form 8829 ignored my profit and no deduction allowed to take. I finally found out (after very detailed and many times testing) that you will need to pull Form 8829, manually enter 100% in Part II item 2 - Percent of gross income from business use of home reported on Schedule C, then Turbotax will calculate the simple way deduction. Hope this helps.
Turbotax: Please confirm this is a right way to fix this problem. Thanks!
