I'm not sure why it's not letting you properly change the user's groups.
Might want to reupload the /admin/showgroup.php and /admin/dochangegroup.php scripts. (I think that's what they are called.)
You can test the status flags by doing this:
UPDATE w3t_Users
SET U_Groups = '-5-'
WHERE U_Number = 'xxx'
That'll update that user, and you can see if the flags are working properly.