I got the same problem, see my other post for explanations.
We receive the payment confirmation while the payment has not been made. Then naturally close the payment window waiting for our license key by e-mail.
Once the payment confirmation received, actually, we still have to find the confirmation button at the bottom of the payment window to make it happen. Then the license key is provided right away.
It is bit strange and I believe it's due to that 2Checkout payment system. It creates confusion and time lost for everyone (client, bank, support) to check afterwards what happened. I would advise not to leave it like that. Apparently we all discover that issue at this point. Probably something new...