Hi Alexandra, thank you for this test and expertise about the problem reason.
To catch the issue with the (default) apache2 configuration I've create a new bug entry: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=511839 I'm not a apache2 expert but done some try and error testing regarding the <VirtualHost *:80> miss configuration. I could not reproduce a problem with multiple VirtualHost *:80 entries within the configuration either with localhost nor with real IP addresses. I can confirm that ScriptAlias and bugzilla3's /usr/lib/cgi-bin/bugzilla3 configuration do not work together if ScriptAlias /cgi-bin/ is defined as first. We should continue the discussion in bug 511839 here. Raphael