You may have missed the check-box to indicate "Religious employment". After entering the amounts on your Form W-2, there is a screen that says "Lets check for uncommon situations". Scroll down and check the box next to "Religious employment". The next screen says "Let's dig in to your religious employment", you should indicate "Clergy". On the next screen you will enter your housing allowance and expenses. Continue through the program to enter the rest of the clergy related information.
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