It really sounds like a problem with the model of the tower then,
the engine has problems finding a line of fire internally although you
have clean visual sight. Might be a little inaccuracy in the intersection algorithm used by ArmA, it seems as if the engine only checks if there is an object between the units to fire upon each other, but not if the units could fire above that object, so the z component is maybe not taken into account. Who knows except BIS, anyway too bad it doesnt work for your mission.