I have a similar issue, using PHP and the FusionCharts js class. I create the chart with code like this:
var myChart = new FusionCharts("Charts/Gantt.swf", "myChartId", "1000", "100", "0", "0");
myChart.setDataURL("index_chart.php?id=1&subId=2");
But in chart.php, $_GET contains only id, not subId.