I don't have a complete answer for you. I'm not very familiar with NIIT. But the IRS instructions for Form 8960 line 9a say to enter investment interest expense "deducted on Schedule A." Could that be what's making the difference? Do you have a deduction for investment interest? Take a look at line 9a with the two different types of deductions.
If that doesn't explain it, compare the two versions of Form 8960 line by line, with the two different types of deductions, and see what the differences are.
