When You Have Multiple Docking Ports Per Ship, You Can't dock?

I have 2 ships that I'm trying to dock. One is the original ship and it has 2 docking ports, forward and aft. The second ship that is being docked has 6 ports, forward, aft, port, starboard, zenith and nadir, similar to the Unity module.

When I go to dock them, nothing happens. No magnetic attraction, no semblance of a dock at all. But if I use 2 ships with 1 port each, it works.

Is this a known bug, and can anyone help me out??!!

Edit: Also, one of the ships is renamed to a station, does that affect it too?