I've noticed that when I place an element (as opposed to a standard track), a long section of unwanted track is placed before my element. It's as if I placed two sections of track, when I only wanted one section. This mostly happens when I am building along, and then delete several sections, going backwards. I am not sure if I am explaining this correctly, I may need a whiteboard and several hours of powerpoint presentations.
That is because pre-made elements will be placed after the next regular piece of track you would place. It's a bit strange yea but just keep that in mind. But this doesn't really have to do anything with the smoothing issues.