You have a remote displacement scoped to two faces. A remote displacement, as it's name implies, creates a remote point which is constrained to it's scoping. In this instance this constraint is changing the stiffness of your structure. You can either apply two remote displacements, one on each face, ensuring the remote point is in the centre of each face (I did this and got 14 Hz for the first two modes), or use the displacement and fixed rotation boundary conditions.
You can visualise spiders/constraints by selecting solution information, then changing to the geometry tab at the bottom of the main window
You also still have contacts to connect the shaft to the rotors. I would recommend using a conformal mesh, contacts introduce additional stiffness that can be difficult to account for.