It's implementing the $ notation for index.template.html, but if you've got prototype in history.js then you should be OK (according to the article), although my French is rusty. If you're getting no JavaScript errors then that would suggest that it's not going to be related to the absence of prototype.
Have you looked at SWFAddress 2.0 as an alternative to HistoryManager? I believe the guys over at deconcept are actively supporting it.
http://www.asual.com/swfaddress/