I believe the program is assuming you are changing the amount for the last 2 months of the year.
Make sure you have put in your full year's income and tax payments, from what you already received and taxes paid plus what you will receive and pay for the last 2 months of 2016. The IRS calculates it so you don't get a refund when you file your taxes. It is hard to say how it work out when you file your taxes but the IRS usually is pretty close.
You can also use TurboTax's W4 calculator, to see what that comes up to
https://turbotax.intuit.com/tax-tools/calculators/w4/
