As a followup to this, if you don't use compact rendering the problem doesn't occur.
So this behaves correctly:
var myDoughnutChart = new FusionCharts("Doughnut3D.swf", "MyChart", "100%", "400", "0", "1");
myDoughnutChart .setJSONUrl("/GetJson");
myDoughnutChart .render("MyChartDiv");
This does not:
var myDoughnutChart = FusionCharts.render("Doughnut3D.swf", "MyChart", "100%", "400", "MyChartDiv", "/GetJson", "jsonurl");