This most likely happens due to a difference between the tree itself and how its leaves work. The tree has geometry, and each physical piece of it has a texture. This geometric portion of the tree is what the mesh modeler takes. However, the tree also has a sprite component to it. You will notice that all the missing leaves are simple 2-D images that don't change their angle relative to the camera; that is, no matter what way you're facing, the images of the leaves look the same, with only their spacial position changing (if that all's confusing, just look closely at the leaves in-game and move your camera around. You'll see what I mean pretty quickly). My assumption is that the mesh modeler doesn't deal with sprites like these, so it just doesn't add them to the item.
I'm not certain about the crashes, though. That could be the mesh modeler attempting to do something it can't, or it could just be the mesh modeler being the mesh modeler and crashing for no discernible reason.