I have a new client who is not an ordained minister but is a member of the clergy with a Deacon title, full time position with the church. The few clergy returns I have done in the past have an amount in Box 1 only on the W-2 and either a statement or housing allowance listed in box 14.

This W-2 has an amount in Box 1 and higher amounts in box 3 and 5 with no withholding for any amounts. TP states the box 3&5 amounts are his parsonage but his former prepared was only subjecting the amount in Box 1 to SE tax. 

I am preparing the return and reporting the box  3&5 amounts subject to SE tax, client is not happy believes only box 1 amount should be subject to SE tax.

Am I missing something? 

Thanks for the help.