Much appreciated. This appears to have solved my issue.
Out of curiosity, is there anyway to have the export respect grouped layers as folders on export?
Great! Automatically not really, but you can experiment with using the "/" character in the layer names, or using slices perhaps. It depends on your set up. Give that a try. Add "/" to layer names before the actual layer name if see if that works for you. So something like this for layer name "Enemies/Enemy001". Let me know how it goes. If it doesnt work out, make a new post requesting the feature.