When you enter your income for all of 2016, Turbo Tax takes each one in the order they were received.

So the first W-2 entered probably didn't meet certain limits, whether it be income, exemption, or deduction levels.  Then when you entered your second one, the income level got high enough to start meeting those preset numbers.  Plus, you are in a higher tax bracket as you file more income.

To test this theory, take both W-2s out of Turbo Tax and try putting them back in in a different order.  The bottom line will be the same, but the interim number may be different.