In Leopard, if you have "Automatically hide and show the Dock" checked in the Dock System Preferences panel, and mail arrives when the Dock is hidden, sometimes the Dock shows Mail's bouncing icon (bouncing out over the desktop from the edge of the screen) and sometimes it does not.
Right after login, if new mail arrives, the hidden Dock will show the bounce. If the user moves the mouse over the Dock when the Mail icon is bouncing, even without clicking, the hidden Dock will then stop showing Mail bounces. This new behavior continues until some other application is started or issues a background alert, bouncing its icon in the Dock.
Other applications do not seem to have this problem, so it appears to be an interaction between Mail and the Dock. It is particularly annoying when you have a Mail rule with an action to "Bounce icon in Dock," yet you cannot see the bounce. There are two workarounds:
Mac OS X Hints
http://hints.macworld.com/article.php?story=20090330170041769