I wouldn't reinstall the Modding Kit as your new scenes seem to work OK. First, I'd back-up your original scene somewhere safe, then I'd export it's height and material maps from a copy you can butcher and then remove terrain. Removing terrain won't effect your entities or navmesh, but it will destroy your paint layers and terrain mesh. You can then reimport your height map. Next set up each paint layer in turn (you'll need notes for that) and reimport each layers material map so you don't need to repaint it. Who knows, it might solve your problem. PS remember to note down your height map's scale and offset when you export it (red numbers flash up bottom left of the editor) you'll need them to reimport your heightmap to the correct elevation.