I am clergy, considered self employed for social security, and turbo tax is not correctly doing the schedule SE, it seems to be ignoring that I paid $0 SS on the W-2.

You may be seeing a bug in TurboTax online.  For some customers, the choice to pay SE tax on "both" wages and housing does not "stick" and TurboTax computes the wrong amount of SE tax owed. 

First, make sure that for W-2 income, you check the box for "Religious employment" on the page for special circumstances, then enter your housing allowance again when asked, even if you already entered it from box 14. 

Then, if your SE tax is not calculating correctly (off both your wages and housing), some people have been able to fix this by deleting the W-2 and starting over again. 

If that doesn't fix it, the only sure fix is to use TurboTax Desktop installed on your own computer from a CD or download, since that does not have the bug.  There is also a procedure to transfer your partly completed file from the online site to your computer so you won't have to start from scratch.