What is happening is the income in box 1, 3 and 5 of your W2 is being taxed as an employee (income tax and employee portions of social security and medicare taxes). Then when you enter your housing allowance in the supplemental clergy interview, it is taxed for self-employment taxes only, but not income tax. This is all proper.
A clergy W2 would not include housing allowance in boxes 1, 3 or 5. The amount would be stated in box 14 on your W2. In this way your housing allowance is not subject to income tax. Then when you enter the box 14 amount in the Clergy interview it is subjected to self-employment taxes only.
If your W2 pay is supposed to be $3000 wages and $25,000 housing allowance, you may need a corrected W2 issued by your employer.
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