While I haven't used 1.9, this is correct behavior under 1.8 when a user is already on a channels access list in a channel, it will move the user from the AOP list to the SOP list, for example. I think it also gives that message when 'moving' a user from the SOP list to the SOP list, etc...
Check that the users aren't already on the access lists for the given channels, and maybe someone can confirm if this is a 1.9 bug or not.