PayPal doesn't check for a specific response to confirm IPN delivery so it's possible it hit your site, got a 200 response, but didn't reach CBSubs. This can happen if something redirects away from CBSubs for example, which we can't really account for. With CB 3.x we'll have some endpoints that function outside of Joomla to avoid these conflicts, but for now we can't really do anything about them. The best I can suggest is navigate to CBSubs > Baskets and mark the basket paid if it's payable otherwise grant them a subscription from CB > User Management.

You may want to verify your IPN URL isn't being redirected away by trying to access it directly. You can also check your servers access log around the time the IPN was sent to see if it redirected away.