It seems organizations are not sent an email confirmation to the person who paid for the registration. I'm not sure if an email is sent to the email address of existing organizations (which may not be the correct person to send it to), but nothing is sent to newly added organizations for event registrations.
This is true for individuals as well, I believe. are you using NXT's event registration forms? because when I used to use database view's event registration forms it would send an e-receipt and it was great