Our application we are integrating into requires an older version of jQuery, so we have a single page that includes jQuery 1.3.2, and the jQuery that comes with FusionCharts. If we omit the jQuery 1.3.2 everything works, but as soon as we include it, the HTML5/JavaScript charts break, but the Flash still works. I've also tested noConflict modes with jQuery and it still breaks.
Also, I'm not using the jQuery plugin for FusionCharts. I'm just using pure JavaScript, however it seems like the JavaScript/HTML5 FusionCharts have a jQuery dependency, even if your not using the jQuery plugin.
Our sample page showing the problem is here: http://iaccutrace.com/fusion.html Notice the JavaScript one doesn't work, but if you reload the page and click for flash version, then it works.