Problem Description: Wrong urls in SharePoint alert message

Recently I ran into a problem with the automatic generated urls in SharePoint alert messages. Each alert message has some hyperlinks in it:

• One to the site where the alert originated from
• One direct link to your alert so you can Modify the alert settings
• One to the item where the alert originated from
• One to the list where the alert originated from

The SharePoint environment was set up with two Web Applications with another authentication mechanism:

• The first Web Application was set up with Windows authentication (using corporate Active Directory credentials): I’ll call it the http://intranet url in this post.
• The second Web Application (extended from the first one) was set up with Forms Based authentication (using credentials in a Forms Authentication data store): I’ll call it the http://extranet url in this post.

For some users logging in using the Web-based form (and hence entering the Forms Based authentication Web Application, http://extranet url), the hyperlinks in the generated alert messages started wrongly with http://intranet. This was not the case for all users entering the Forms Based Web Application: for some the hyperlinks in the alert messages started correctly with http://extranet.