I found this in the documentation while researching something else:
To register the chart with JavaScript, we set the registerWithJS parameter to 1. It's the last parameter in FusionCharts constructor function.
For example:
var chart1 = new FusionCharts("Column3D.swf", "chart1Id", "400", "300", "0", "1");
This helped in my particular situation, however the sample already had this and still doesn't work.