[Solved]-Highcharts backgroundColor for multiple charts is only applied to one chart-Highcharts

You are doing it wrong, chart2 is not an option. Change this :

$('#container2').highcharts({
    chart2: {
         backgroundColor:'Transparent',
         size:'100%'
    },
    ...
});

To this :

$('#container2').highcharts({
    chart: {
         backgroundColor:'Transparent',
         size:'100%'
    },
    ...
});

See the updated jsFiddle