I think you have made a mistake somewhere. What are the codes in box 7 of your 1099-R, and did you enter those codes correctly? Also, is this an IRA, or a qualified plan from your denomination (such as a pension, a 403b, a 457a, or something similar)? It is important to understand that you can only have a clergy housing allowance if your retirement account or pension is administered by your denomination. If you rollover your funds to a private IRA, you lose the ability to have a tax-free housing allowance.
