Without the files, my guess is that the scene is saved with an active section cut, but the style does not allow display of section cuts. You place the scene in LayOut and it's OK. You change the style in LayOut to one that is set to allow display of section cuts. Now you see the cut. That's the only way I can duplicate what I think you are saying. All styles are edited within SketchUp, even the ones you select in LayOut (they're the same).
and I agree it's can of worms, ball of wax, whatever.