“maybe you use too many very short pieces of track?”
No, I tend to use as few pieces as possible and make them quite long. If you’re editing parts then invariably you will end up with some short pieces, but the game should be able to cope with this.
When you’re adding track and junctions you don’t get any visible indication of track joins, so if that’s what’s preventing some of these things working then that needs to be changed. From a player’s perspective once I’ve laid out a whole section of track it shouldn’t matter if it’s stored as a set of different length splines (or whatever) – track is track and I want to be able to work with any part of it the same way as any other part.