Is there a way to display that a user has new messages waiting when they log in?

I have a trick for you. If you wanna put all your alert in one module :

1 - download the cbworkflow mod
2 - copy the cbrlogin module
3 - put them both in the same module position
4 - unpublish avatar, and other message that you don't need
5 - hack the file, removing the logout button (you can't add a link if you still want somewhere the logout feature).