Hi,
I had a quick look at your structure. The Vias in your model are Vacuum. Are you sure this is correct? Furthermore the Ports 2 & 3 are directly located at a GND bridge. Because the GND bridges are not connected with the main GND (vias problem) the port mode solvers sees some "floating" metal plates right at the port. Please change this. Finally, I would move the ports 2 & 3 away from the bridges anyway. If the bridge is finally connected the port mode solver will calculate a mode which includes the bridges. This will certainly vary from your CPW mode. Whenever you have something like this it should be INSIDE the structure and not right at the port.
F.