I think the add on does not support cycles textures yet. But could be wrong about that.
About the baking: When Blender renders the baked images, you might need to save them first after baking. Before you do that they are only in memory. This issue occurs with a couple of workflows. Not sure it will help, but sure worth a try.
I also had some problems when I was working with UV mapped (regular not cycles render) textures and the addon. The solution was that the addon creates a new UV map with the new arranged texture images and I got it all mixed up. I then deleted all the UV maps I did not want except my original and then restarted the export process. Worked then.
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