To clarify, when i select on the 2 docked ports. the one on the main ship side gives me the option to Undock but i get no action when i press it. That option disappears but the ports stay attached. the mated port in the attached ship does not give me the option to Undock but as i have checked other docked ships this seems to be normal. However it shows Locked before and after i have pressed the Undock button on the other port. And no struts on or near ports and they are the Clamp-o-Tron default ports.
I loaded an old save from weeks before the issue started and this issue now exist in that instance also. This affects all docking ports on all of my current ships.
But to add a level of ???? if I build a new ship the ports function correctly but they give the the option to decouple node and not undock until i have separated them once and then redocked. But even after that they still function properly.
I can't seem to get the debug window to come up using alt-F12 or alt-FN-F12 but if this is unrelated it is for another time.
I am going to look into "bewing's" answer and see if this helps.
Thank you all for your post!