Shame you have to have apps open to show in notifications

[ubercool]

My Messages notifications show up in the Notification window, i.e. not pop-ups, despite the app being closed. Also noticed that there are no badges on Messages in the dock.

 

[Krazy Bill]

Set these "notification" apps to start up at log in. Check the "Hide" box if you don't want to clutter up your screen with them.