There may be a bug in Turbotax Online's handling of the housing allowance. For some customers, the choice to pay SE tax on "both" housing and wages doesn't "stick" and the program only calculates SE tax on wages. I think it's a bug but Turbotax believes is it user error. It seems to happen mainly when you are importing last year's file that also had a housing allowance.
Some customers report fixing the problem by deleting the W-2 and entering it again. Make sure you check the box for "Religious wages" on the page of Special Circumstances, and enter your housing allowance again when asked, even if you already entered it from box 14.
If you are self-employed, you must use job code 813000 to tell the program you are clergy and activate the housing allowance questions.
Otherwise, I recommend switching to Turbotax Deluxe installed on your own computer from a CD or download. In addition to being most cost effective for most taxpayers, the desktop version doesn't have this problem, and it allows you to directly inspect and edit the tax forms and worksheets so you can verify your schedule SE income and other items. You also need the desktop version to fully take advantage of employee expense deductions under the Deason rule.
