In 13.04 I am experiencing the same. When I click the X to close xchat the close dialog opens and I check the box to mimimize the tray, but instead it seems to go away. When I look in the notification area xchat is there, but not marked as already running. When I click xchat it opens a new window and logs in as one of my backup user. However, the previously opened xchat still seems to be running in the background somewhere. (In the new xchat instance I can see my other user still active, even after an hour or more of the previous xchat instance disappearing.)
In 13.04 I am experiencing the same. When I click the X to close xchat the close dialog opens and I check the box to mimimize the tray, but instead it seems to go away. When I look in the notification area xchat is there, but not marked as already running. When I click xchat it opens a new window and logs in as one of my backup user. However, the previously opened xchat still seems to be running in the background somewhere. (In the new xchat instance I can see my other user still active, even after an hour or more of the previous xchat instance disappearing.)