Beams will also be cut in 3D when they cross other beams, walls and columns. It depends on their beam priority number (set within the beam tool), wall priority number (set within the wall tool) and the 3D Intersection Priorities (set via Options>Project Preferences>Construction Elements).
Is it possible any of these elements are interferring with your beams, even if they are on hidden layers?
Cheers,
Link.