How strange, I've never seen this on my systems, either Windows XP or 7. For ne the alerts simply appear for several seconds and then close...
Not sure if this will help, but there are numerous ways to disable notifications form the System tray, one of which is to edit the registry.
To disable balloon tips in the notification area, follow these steps:
1. Click Start, click Run, type regedit, and then press ENTER.
2. Locate the following subkey:
3. Right-click the right side pane, create a new DWORD value, and then name it EnableBalloonTips.
4. Double-click EnableBalloonTips, and then give it a value of 0.
5. Close Registry Editor.
6. Log off Windows, and then log back on.
There are also a whole host of utilities for doing this too.