RazanG, would the solution in this post
Also, I found that in paying for S's applications, the payment did not show up on the Common App website unless I first clicked on a little "Finish" button on the lower right on the NetPay page. Not sure if that's your problem, but thought I would mention it.
As to the effective date -- for all S's payments, although NetPay showed an effective payment date of 1/4/10, the Common App shows that the payment was submitted on the date (12/31/09) that I made the payment online. For the one college that required that payment be made before the app could be submitted, there was no problem submitting the application.