You said you downloaded these meshes right? If so I don't see why they would not show up unless their object group was overrided by any other objects. As far as I know, the new objects in the MyTrees, MyRocks, etc. will not show up if the new .fhos are replaced with older .fhos of the same default groups. Therefor you put those new objects from the (MyTrees, MyRocks, MyPlants) into a new custom object group you've made. This could be the same for the trees and bush problem you are having. Make a new custom group for the certain ones you used for the map, and as for the placements in your map, go to your *MapNameHere* folder in your terrains folder and seek out the *MapNameHere*Objects.cfg. You will see a ton of strange numbers but don't be intimidated. Just change the group name of the custom trees you used to the new custom object group you put the trees in and then click save. Then after this try exporting the map.