*** UPDATE ***
I was made aware of a fix in SP1 that should cover this issue. http://support.microsoft.com/kb/941422
SharePoint administrator beware!!! You must manually recreate your web applications (with the exact naming as compared to what was backed up) to ensure that all the timer jobs for each web application is created when restoring from a SharePoint backup. The problem seems to be the automatic SharePoint restore that restores the databases and web applications must not follow the same method as if you were to do it manually because the automated restore does not create the necessary timer jobs for any web application restored. This includes immediate alerts, so if you have done a restore and you are wondering what has happened to your alert emails and your assigned-to emails it is because the restore didn't do a proper job.
Of course the recommendation for getting the timer jobs created and associated with the web application is to manually create the web applications BEFORE you restore. The problem is you might not realize there is a problem until after a couple weeks / months after your restore. Now you have to delete the web applications, create them manually, and restore from the last full backup.
Here is the Microsoft KB article that discusses the issue.
http://support.microsoft.com/kb/942989
Here is the link to my work around and fix for the issue that is less intrusive than running a complete restore of your farm.
/llowevad/archive/2008/02/18/workaround-for-creating-timer-jobs-after-a-restore-in-sharepoint.aspx
dwollerman