[geoschmo]

What's on the PBW server or not shouldn't matter for what you see on your screen. But where the files were on your machine when you created the empire does matter. Custom race image files should all be in a named subfolder under the empires folder. If they were somewhere else when you created the empire, like in the root empires folder or the root pictures/flags folder that might explain why it's having trouble finding them now with the new version.