Glad it seems to have sorted itself out. Hope it continues to work. Strange though.
Did you get the tgo to work as well? As far as I know tgo's don't reference mtl files, those are for obj files only. When you get errors like missing files when you load a scene you can select Project > Show Project Assets to find out exactly where the problems are. If the files are in the right place then maybe the shader is looking in the wrong place . . . in that case just fix the file paths and re-export the tgo. You can use relative paths, meaning that if the textures are in the same folder you just need the filename and extension. That way they'll always work even if you move the folder.
Saving out object references as tgo's is a good idea and worth the trouble. It eliminates the need for a sidecar file (mtl), and the shading network that you create in Terragen is saved along with the object. Plus it's compressed.
Unfortunately some third-party models can be the source of a lot of problems. Hope you're able to get all 108 of your models fine-tuned and placed successfully in your scene.
FYI in response to a previous question, check out
MeshLab, which runs on all platforms. The interface can be a little daunting but it's a great tool for fixing bad meshes. Not sure if it can be used to merge material groups, but it might be worth a look either way.