There is a bug regarding how SE tax is calculated. It may also affect the excess housing calculation, although this is less common and I have only seen two reports, compared to many more for the SE tax issue.
What seems to be happening is that the choice to pay SE tax on "both" housing and wages does not "Stick" and reverts to one of the other choices.
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.
