I have the same problem with this code:
FusionCharts.setCurrentRenderer('javascript');
chart = new FusionCharts(base_url + "js/fusioncharts/Charts/MSLine.swf", "ChartId", "800", "400", "0", "0");
chart.setXMLUrl(base_url + "js/fusioncharts/Charts/Data.xml");
chart.render("chartDiv");
As soon as I remove the setCurrentRenderer call, it works fine (as a flash chart).
Firebug gives this error: "NetworkError: 404 Not Found - http://localhost/XXXXXXX/http%3A%2F%2Flocalhost%2FXXXXXXX%2Fjs%2Ffusioncharts%2FCharts%2FFusionCharts.HC.js",
so apparently the path to the js file gets broken somewhere in the process