I’m actually having a similar issue. In my case, the member is created, however there was no e-mail address set in the DB. Therefore, I never received a conformation e-mail with the registration link. I went into subscription_handle_debug.log and copy/pasted the URL for now. Obviously I need to figure out what the issue is, though. Any idea what it could be? (The member is created with the correct membership type, btw.)
Edit: In addition, I just realized that, though I have the option set to create a WP user also, it only does this for the “free” membership level. Paid users do not have a matching WP account created.