Is there anything common between the users that it's failing on? Things like UTF8 characters in name, username, or email or even the time of day those are being paid. Are you receiving IPNs from PayPal regarding those payments in CBSubs > Notifications? Any errors or further information regarding that basket in CBSubs > History Log?
In these cases, the payment transaction is successful and the payment basket shows as completed and the subscription is active, but the membership plan activation actions are not being triggered.
To compound the issue, it is very difficult to manually activate the subscription when Community Builder/CBSubs shows the subscription as active and the payment basket as completed, but the user is not enabled, has not been assigned to the expected user group, activation email is not sent and the other plan integrations have not been triggered.
These 2 statements are confusing me. So the subscription is becoming active, but none of its integrations are firing? This sounds like something is interrupting and messing with the user store process. It is likely entirely related to your below topic.
www.joomlapolis.com/forum/255-developer-members-support/244213-1062-duplicate-entry-xxx-xxx-com-for-key-email-unique#325990
If that's happening also during the PayPal payments that's a fatal SQL error and will stop everything.