I can confirm that it is still reproducible in Karmic too. It is observable with Skype and Pidgin, which close their windows but remain running in the notification area. Whenever these programs' icons get a click in the notification area they show/hide their windows, but whenever the windows gets shown they are always redisplayed a little bit lower and a little bit to the right until they reach the bottom panel.
I can confirm that it is still reproducible in Karmic too. It is observable with Skype and Pidgin, which close their windows but remain running in the notification area. Whenever these programs' icons get a click in the notification area they show/hide their windows, but whenever the windows gets shown they are always redisplayed a little bit lower and a little bit to the right until they reach the bottom panel.