If you are a pastor and performing religious duties, then you are self-employed for income tax purposes and you should not have social security and medicare taxes withheld. You will still receive a W-2 as a common law employee but boxes 3-6 will be blank. If they are not blank, then your employer is treating you as a regular employee (like a secretary or maintenance person) who does have SS and medicare tax withheld even when working for a church.
If you check the box in turbotax for religious wages, but you have box 4 and box 6 taxes, turbotax will get confused and not do your taxes properly.
Your church may be paying you as a lay employee even though your title is "pastor." Titles are not important, what makes you a clergy person for IRS purposes is a 4 point test; you administer
the sacraments, are considered to be a religious leader by your church, conduct
worship services, and have management responsibility in the control, conduct,
or maintenance of your congregation. You don't have to meet all 4 tests strictly, but those are the factors. If your church is paying you as a lay person, then don't check the religious wages box. You would subject to the normal tax rules for ordinary workers instead of the special clergy rules.
See this for clergy tax issues. Then check with your church treasurer, or denominational tax expert, or a tax professional who understands clergy wages, if you need clarification. http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdf
