Stop creating users outside of CB. I'm sorry, but that's your only reliable solution. We are not going to allow user synchronization to be ran regularly, because it shouldn't. User synchronization bypasses all of CBs registration checks (approval and confirmation), CBSubs, and more. It is not meant to be used in the way you are using it.
We've plans to see if we can create users in CB when a new user is created by Joomla outside of CB, but there's no guarantee that'll even work depending on your extensions usage or if I can even get it working in a way that doesn't flat out break all of CB. Even then they'd be unconfirmed and unapproved with incomplete profiles (all required fields skipped, field validations skipped, etc..). Below is the feature ticket regarding this.
forge.joomlapolis.com/issues/5306