Clergy Taxes

I was hired on as a family pastor for the past year. The church has a lot of red tape to bring on new employees, so they considered me an independent contractor. I received a 1099-MISC, and just entered it into Turbo Tax. According to the calculations, even after taking into account my housing allowance, I'm getting back thousands less than I did last year. 

 

As an experiment, I entered my same income in a W-2, and Turbo Tax calculated a tax refund thousands of dollars higher. Why would this be?