The permissions check in _popups_reference_links() of user_access("create $add_type content") doesn't work for content types created by modules that don't follow the naming scheme of node module. Webform module is a prominent example.

Instead, perhaps you could call module_invoke_all('access', 'create', $add_type); ??

I'd submit a patch, but my version of popups_reference is too hacked up at the moment. Hopefully this will be enough for someone to fix the problem easily.