See http://stackoverflow.com/questions/13929394/unable-to-change-presence-status-of-my-user-with-smack where a users modifies the Presence instances returned by Roster. Since those are not clones (and not immutable), those modifications are done directly on the internal state of Roster and persistent.
Roster should return copied presences instead (at least until Smack has immutable stanzas, which appears to not happening anytime soon).