Ok, your simulation is fine. I overlooked an important detail.
Z11 is only equivalent to input impedance when there is only one port. You can see this in the definition of Z-parameters; it involves assuming that the other ports are open-circuited, not matched. When you add a second port, obviously Z11 is going to change!
You can confirm the ports are both well-matched to the line by observing S11, S12, and S22. Alternatively, you can derive the expression for Z11 of a two-port network, and confirm that it matches what HFSS is showing you.
Good luck!