New member application verification issue

Since transitioning over to CB Paid subscriptions, we've had an issue where applicants are unable to verify their email address.
In the section of the verification email sent to the applicant that used to contain the link to verify the address is this message in html: <br/>Email address is already confirmed<br/>
The application shows as being unconfirmed in the back-end.

What has changed that would cause this? How can we fix it?

That should only happen if the user is already confirmed or they don't have a confirmation code. How are users registering? Please be sure you're using CBs registration form and not any other form. Is cbactivation empty in the _comprofiler database table for that users row? Does registering without a subscription send a confirmation code or is it purely when registering and purchasing a subscription at the same time?