I was using shared tracks for multiple trains and lines, but small changes / additions would affect every single line which used the shared track, causing a bit of a headache to sort out.. in the end, I made it so each line has its own exclusive track.
I still have a central 4 station platform which has trains (lines) entering from both sides for each platform, but even this can mess up causing all trains to want to swap tracks (if a crossing exists) and a change is made, causing a nightmare on the lines.
I didn’t realise what was going on at first but after some playing around realised that all the lines recalculate their paths when you make such changes.. you can force a recalculation too with different results.
See the images here: http://www.train-fever.com/forums/topic/waypoints-desperately-needed/#post-11462