David,
in the latest releases, you have changed Anyrail such that when you add a new Feature, it goes on top of any other already in that space.  I found this to be a problem where I had added a road and then tried to add a bridge over the track, but under the road.  It put the bridge on top of the road creating the issusion of a tunnell!
In other software I have used, there was an option to "move an object back a level", move the object forward o level", "bring object to the fromt" and "move object to the back".
This could be an improvement you could make to Anyrail so that the user could determine which Feature goes on top.

Charlie