I've run into this several times recently. Symptoms are very similar to the reported KSP bug, but it's impossible for me to tell for sure as I would need to edit the save game files. KMP stores them in the DB, which is abit out of my understanding to look at. I'd never run into this before in over 200hrs of playing solo KSP, but after just a few hours of KMP I hit it several times. I can only assume that something in KMP is aggravating the underlying issue in KSP. As far as fixing the problem, I've not found a solution. But, I have figured out a few things: 1) I've never had it happen to ships that were docked in the VAB (built docked) 2) It seems more likely to happen after a time warp or a disconnect (I believe when you disconnect, your subspace is "time warped" to server latest?) 3) After docking, undock and redock a few times seems to prevent it. 4) Having some sort of command module on items docked helps prevent it (I was trying to dock a fuel tank, then decouple the command module/rcs/batteries/motor to leave only the tank. It failed every time until I left one of the small probe modules on the fuel tank.) 5) Attach every docking port with a decoupler. At least if it bugs, you can separate it the ships still.