New Clamp-O-Tron Sr. Won't Dock! WTF?

[Danger Will Kerbinson!]

I've had this same issue on a new station, however it affects ports of all 3 sizes.

Its a station with 4 identical arms projecting from a center stack, these arms each have one docking port of each type and the arms were placed using symmetry of course because I'm not insane. The ports on 2 of the arms work fine, the ports on the other 2 do not work. Other connected items like lights work so I assume the game sees them as connected to the station. Could not tell you if these arms will transer fuel...because you can't dock to them. Its just like some of the ports dont have any juice turned on, bump them all you want and nothing happens, move one arm over and shazam it works.

If this were the persistance file in my case would it be possible to have a different state for identical parts on the same ship?

My solution was to crash it into the ground and start over which is probably less than ideal.