$wgAutopromote doesn't actually put the user into the group; it just sometimes pretends the user is in the group when checking rights (and on Special:Preferences). Ignoring whether this behavior actually makes sense, what's not working for you? The user should have the rights associated with the group, even though he won't be listed in it on Special:ListUsers.
What version of MediaWiki are you running? Do the desired rights show up for the group on Special:ListGroupRights? What is the exact code you're using with $wgAutopromote?