We are about to release Ardour 4.0 in which all of this has been reimplemented. I suggest you test the current pre-release version from nightly.ardour.org to see if this issue still exists.
Hey Paul, thanks for your reply. I finally managed to recheck this layering behaviour using Ardour 4.0.111+r12337. After loading one of my Ardour 3 projects I experienced the very same behaviour: http://www.niklasliebig.de/temp/Ardour4.0.111_Ubuntu14-04_Layering_Issues.mp4
However I was not able to provoke it on a fresh Ardour 4 test-project. So hopefully this bug won’t appear at future projects. Still, the layering disorder seems to be stored within my Ardour 3 project files and gets adopted when continuing work with Ardour 4.