Managed to resolve this by...
Registering with the JS as the documentation mentions... (over sight on my part)
var myChart2 = new FusionCharts("Charts/AngularGauge.swf", "myChart2Id", "320", "320", "0", "1");
Then in my funciton, calling:
var refToChart = getChartFromId("myChart1Id");
refToChart.hideLog();