It is defined as a second site in Mojo. Mojo is running under localhost, so I added this site using the name of my local machine: development.
Perhaps it is not recognized as an intranet site and therefor is effected by the IE settings for Internet sites. But then again, the old site was running on another machine.
window.alert was inside the popup function. Adding 'javascript' does not seem to be necesary. I develop and run everything in Windows (XP or Server 2003).
Perhaps you could try a test on your environment?
Jan