I have ran into this same issue.
Renderer: Javascript
Chart: Bar2D / Stacked2D
jQuery: 1.8.2
FusionCharts.js: 3.2.4-release.8565
HighCharts: 2.1.9
Once I resize the window the colors appear. Flash charts have no problem rendering the colors.
I am not defining the pallet colors and opted for no gradient color on the bars.
Any assistance would be appreciated.
M