Sounds like you had other fatal issues present that stopped GJ half way through its process. Next release will have better tools for "mass fixing" various issues, but I can't account for other extensions or plugins causing problems. You should ALWAYS be running your site with debug mode enabled and maximum error reporting configured in Joomla global configuration while testing and debugging or you won't be able to see if something is silently failing. A single fatal php error before, during, or even after could cause GJ to fail or anything else for that matter.
As for the forums that's exactly what it's supposed to do. It's supposed to create a new Kunena category for each group. You can disable the forums on a group by group basis through.