Well, is your downloaded objects in a default group such as MyPlants, MyRocks and stuff like that? Yeah, remove them from those groups and make a new group for them to add them to.
Also, for your first problem there, did you try uninstalling and reinstalling? If you do, then make sure to make a folder to put all your custom/downloaded stuff including .cfg's such as emotes.cfg and music.cfg, and stuff like that and media, screenshots, exports, folders in, and also my_presets and presets. Make sure they are organized in the other location on your computer you have them in! ^_^
And did you try restarting the game and logging back into the map itself? Or switching rendering systems?
Hope this helped, and the way my post helps is Map, Character Tex Issue, and then lastly map, lol.