After installing Office 2007 SP2 some users are having problems with desktop alerts not working.

There is a bug with the Desktop alert that affects some users. The users report that when new mail arrives as Outlook first loads, the desktop alert won't work until Outlook is restarted. If no new mail arrives as Outlook is first loading, the alert works on later Send/Receives, at least for a few hours. Microsoft is aware of the problem.

Workaround

Some users discovered that disabling the "Outlook Change Notifier" add-in appears to have solved the Desktop Alerts issue. This add-in is from Apple and used with their mobile device service. If you need the add-in for syncing, you'll need to wait for an update to the add-in.

If you don't have this add-in installed, our usual troubleshooting advice stands: start Outlook using the /safe switch. If the problem goes away, enable and disable add-ins until you identify the culprit. While the /safe switch does more than just disable add-ins, few users are affected so it’s more likely an add-in causing it. In fact, in a case like this, I would probably skip safe mode and disable all non-Microsoft add-ins and see if the problem goes away. Re-enable the add-ins one at a time based their importance to you and see if the problem returns.