If you modify the scale of an entity and save the map, when you load up the map (either in game or in editor), the scale will have reverted back to default size. If you go into the editor and then fiddle with the problem entities, they'll pop back to what you've set them. They still won't save of course, but clearly the editor isn't discarding the modifications entirely.

For whatever reason the editor just doesn't seem to actually apply the modifications.