If you are using Plus! for the notifications aswell make sure you got both options ticked:
![[Image: attachment.php?pid=829310]](http://shoutbox.menthix.net/attachment.php?pid=829310)
Or set a different one for the notifications (for those contacts, for some or for all contacts) if you so desire.
Otherwise make sure it's still set in messenger preferences:
Tools > Options > Alerts and Sounds
...make sure "display alerts when contacts come online" is checked and along with that you may want to untick the sound for "Contact Online" to have sound only for those you've set one for through Plus!
The appearing offline could be they are on "appear offline" or because of serverglitches.
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