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There is a bug affecting some clergy where the choice to pay SE tax on "both" housing and wages does not "Stick" and the program reverts to one of the other choices, resulting in incorrect (too low) SE tax being calculated. This may be related, although I haven't seen this exact symptom reported before.
Some customers have reported fixing the problem by deleting the W-2 and entering it again. Also, make sure you enter the housing allowance on the screen that asks for housing allowance and housing expenses (in the W-2 interview after checking the box for "special circumstances.") Even if the housing allowance is in box 14 of the W-2, it needs to be entered again on the later screen.
The only other solution for now is to change to using turbotax installed on your own computer from a CD or download, since the problem seems to only happen in Turbotax online. You can transfer your partially completed tax file from your online account to your computer so you don't have to start over from scratch.
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