TurboTax is not designed to handle the situation when you are a non-clergy employee for part of the year and a clergy employee for part of the year working for the same organization. You will have to make certain manual adjustments, or see a tax professional this year.
Another user may be able to answer, although I seem to generally be the clergy expert. I'm traveling right now, so it may be a while before I can put all the details down in writing. I will get back to this eventually.
