Housing Allowance for Pastor and W2

Hello - I'm a new pastor. I received a W2 from my church with my total wages. In a box (14) on the W2, I'm given the total of the housing allowance I received for 2017. The total in box 1 includes the dollars appearing in box 14. As example, I received a housing allowance of $2500 as a portion of my total compensation $40000. $40000 is in box 1 and $2500 is in box 14. When I enter these into TurboTax, my tax burden actually goes up based on the housing allowance, which doesn't seem right. My question is: should my church have included the $2500 in the $40000 or should I have received a W2 that said $37500 in box 1 and $2500 in box 14? Am I double counting the income in some way? Any help is appreciated. 

Richard