I ran into the same issue and was on the phone with TurboTax for a while trying to figure this out. TurboTax was correct.
I had capital gains that were taxed at 15%, while my tax rate was 22% this different tax rate on a small portion of my income made just a slight difference in the amount of taxes owed.
Something I figured out was where all of the numbers come from when looking at my return.
If I go to my forms list, and then highlight line 16, it gives a spyglass to go to supporting form. On my Tax Smart Worksheet, I could right click on the Tax amount and select Data Source. From there I could see that number listed next to Schedule D Tax Worksheet Line 47, and by clicking there I could see the TurboTax number on line 45, and the Tax Table Calculation on line 46. Line 47 is the lesser of the 2 numbers, and is used to calculate the taxes owed.
This is a bit long-winded, but I hope that it will help someone out. I delayed filing taxes for 2 weeks, because this bothered me, and I couldn't figure out why the numbers were not what I thought they should be.
Net result is that TurboTax saved me money, about $200, that I never would have found if done by hand.
