Looks like some still do it the old way. I was able to "fix" this issue without reloading, though this solution only helpful for manned crafts.
Install KAS/KIS
Switch to craft, Click 'undock' button on working dock port.
Get an engineer (equipped with a screwdriver) close to the joint, hold attach/detach button (default 'H') and click on the malfunctioning docking port.
Always works as clock for me. Can illustrate if you ask.