Yes, the solution is to load jquery and highcharts just before the closing </head> tag:
Does this help in your case?
Normally, these files are loaded by Fusion Charts after the onload event is fired. Our PDF tool uses some heuristics to detect long running onload scripts and if the files take too long to download then the script is aborted and the charts are not created. The code above causes that the files are loaded before the onload event which should ensure that the charts are created.