The difference in the amount is due to how NTS accounts for World Evangelism Fund (WEF) payments. By default, NTS assumes that you will make your WEF payment in full. Therefore, NTS applies the amount due for WEF as an exemption for Pensions and Benefits (P&B). With this exemption applied, it reduces the amount due for P&B.
The Funding The Mission site does not make the same assumption. It only applies the exemption after the payment has been made. Example: A payment is made for the full amount listed as due for WEF and P&B on the web site. After posting the payment, the web site will indicate that P&B has been overpaid slightly. This is due to the exemption that was applied with the WEF payment.
If you pay the amounts NTS says is due, then you will be paying the exact amount due and nothing over. (This is true if the Funding the Mission web site and NTS are both showing the same income.) For situations where you are paying more or less than the amount due for WEF, please see the link below.