Oh, this sounds rather nasty. First time hearing such problem.
Tracks and buildings should not cause any problems to this mod.
Can you first check the filters?
Be sure "Toggle show all trains" and "Toggle show trains on all surfaces" buttons are both selected (thus both buttons are illuminated).
Then open up the filter panel (clicking the upper-right" funnel icon) and be sure all filters are empty. (The "Layout" filter should be "Any".)
If this does not work, then it could be some real bugs.
Then please try with some older saves or some new games. See if the GUI can work properly.
If all above fails...
After you tried removing this mod, did you save the game first? (So the game file is in the state of NOT having this mod.)
THEN reinstall this mod and load the game file.