I just had a similar problem. I tried a few solutions all at once, so maybe one of these will help you.
1. Make sure the entrant clicks the "return to This email address is being protected from spambots. You need JavaScript enabled to view it." link after paying. Not sure but I think this might be necessary for the record to get saved.
2. I received a notice from PayPal saying that the IPN was failing. I have Akeeba's Admin Tools component running so I added .paypal.com to the whitelisted domains.
3. I am integrating with Community Builder. I used its tools to check the database and found a problem with the user database. I followed the directions to fix it.
I ran a test with PayPal in test mode and it seems to work now. I will post again if I have further problems.