Wrong urls in SharePoint alert messages

Recently I ran into a problem with the automatic generated urls in SharePoint alert messages. 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.