The lab parts are VERY slightly narrower to fit in spaceplane cargo bays.  It should have no effect on your station.  If you have any parts surface attached to your labs than there might be a small gap between them and the surface they are attached to.  Also if you have any parts attached to the cyclotron or the Pectromatron they might not look like they are placed properly due to the changed collision meshes. Like Ethernet said, it should only be a minor visual problem.