Hi, I'm using FusionCharts with DNN and I don't have any problems after instaling module on web server. First I developing module on local server, just like you. 
  
  
  
Maybe you got something wrong with paths? To generate chart html I always using ModulePath property, for example: 
  
 
var html = FusionCharts.RenderChartHTML(ModulePath + "Utilities/FusionCharts/MSCombi3D.swf", "", xmlData.ToString(), objectID, width.ToString(), height.ToString(), false, true);
 
  
  
  
Leave your code here, I'll try to help you. 
  
  
  
Kind regards, 
  
artek