Yes, there seems to be an issue with certain models compiled by MDLEdit on Linux for some reason. Fortunately this can be resolved by importing the model into KBlender and re-exporting. It will be addressed in the next full release, but I'll see about pushing a hotfix for Linux users in the meantime.
One thing that was particularly helpful for me when I reskinned modules is the ever handy Rename Master, a utility that can rapidly rename hundreds of files.