Kerbal Space Program

I also have a problem with this, though once a port is jammed there is no way to release it. I can't re-create this bug reliably despite trying all day. It doesn't seem to occur on land - but only in space. I've also only ever had it happen with the normal sized docking port. Here is a screenshot and a list of steps I performed when the bug occurred.

Note: All modules were sent up on a launcher which attached the module through two large docking ports, and then undocked from the launcher.
1) Habitation Module sent up into orbit around kerbin
2) Tug sent up and docked with habitation module (large port)
3) Solar Array sent up, tug undocked and docked with solar array (normal port). solar array + tug docked with habitation module (large port).
4) Fuel storage sent up. Tried to undock tug (normal port) from the solar array but couldn't. Docked the entire station to the tug (large port).

I note that the electricity from the Solar Panels and generators does not reach the illuminators on the fuel storage to keep them illuminated constantly, so it also appears that crossfeed for electricity is not working when docking ports break - however I can pump fuel through the bugged port. There was a lot of kerbals moving around to and from the tug, and swapping of controlled ships, as well as time acceleration.

I am using a myriad of mods, but none which alter the docking ports, electricity or fuel transfer (except perhaps Kerbal Attachment System, though this shouldn't affect the port).

If you have any questions for me about this scenario I'll try my best to answer them. I still have this save-file but the large amount of mods would detract anyone from loading it.

EDIT

More information:
Undocking the habitation module first fixes the normal ports, allowing me to release them. Doing this does not fix the flickering lights.
Undocking the fuel tank first does not fix the normal ports. However the flickering lights on the fuel tank are fixed (that module has its own power supply).

Summary: The solar array to habitation array dock prevents the solar array from undocking with the tug.
Suggestion: Seeming as when two ships are docked, only one of the docking ports has the options to "undock" and "disable crossfeed" I wonder whether this affects the docking bug.
Scenario: My current module from the picture goes:

Fuel Module : Undock Port : Port : Tug Module : Port : Undock Port : Solar Module : Undock Port : Port : Habitation Module.

I managed to re-create this scenario on kerbin using vehicles, but again couldn't reproduce the bug. I can't tell whether it's related or not, but this configuration only occurs when you join a ship with a docking join in it, with another ship with a docking join in it.

Notes:

Often when docking the habitation module, which causes the problem, if you are controlling the habitation module when you undock, and then swap ships back to the station, the station suffers from the spontaneous explosion/destruction/spin bug. If you control from the station and undock the habitation module, then everything occurs as stated above. [b]This bug may have a relation to the ship focus switch spin bug[/b]