It seems that you are using the export handler that is designed for exporting Flash charts only. For exporting JavaScript charts, you would need to setup export separately.
The .NET export handler is not yet equipped to handle JavaScript charts. Having said that, you are not out of luck yet. There are two options you still have:
Use pure server-side rendering to generate chart image - http://blog.fusioncharts.com/2013/03/how-to-save-charts-as-images-at-server-side/
Use the CodePlex SVG rendering engine for .NET after sending the chart's SVG data to server - http://svg.codeplex.com (You can get a chart's SVG string, even on IE, using
chartInstance.toSVGString()
)
Note that if you are using PHP export handler, it can handle both flash and javascript export using the same export handler as mentioned in the documentation article - http://docs.fusioncharts.com/charts/contents/exporting-image/ECPureJS.html