I just took a peek at the source - it has not been modified in 9 months, so it can't be related to any recent code changes.
Also, all the deletion code is local to the file, so changes to an external file wouldn't cause this either.
When you delete the event from the Respond To Events screen, do you get a message at the top of the page: "You are not authorized to modify installation."? If not, do you get the message: "The event handler was deleted."? This would help in troubleshooting.
Also, does it delete correctly if you go to Advanced->Configuration->Events and use the delete from there?