When I've created custom statuses in the past we always run into the issue of the custom columns live in the document so the document determines which ones are visible, including custom statuses. To load the statuses into an existing pdf, you have to go into the custom column dialog and import the CustomColumn.xml file. I'm not sure if this helps, but if you can script the import of that file, you should be good to go. This is only an issue with pdfs that were previously opened in a different Profile, so hopefully, the problem fixes itself over time as users are all on the current Profile.
