I have the same bug, reproducible. The only mod I'm using is KerbalEngineer Redux, which I will try removing when I get the chance. For me, the bug started when I docked to a strange vessel -- I had a little probe built onto my science station attached by clamp-o-tron, Jr., but I built it wrong so when I decoupled the clamp-o-tron the probe stayed stuck and wouldn't separate. Then later I added a docking port to the science station by bringing up a claw adapter, with claw on one end and clamp-o-tron, Jr. on the other end, attaching it to the stuck-on probe of my vessel. Now, whenever I try to dock or undock, the game goes nuts. As I cross some invisible boundary of a couple Km distance, either entering or leaving, or if I enter time acceleration inside the bubble together, whichever vessel does *not* have the focus gets wildly shaken (small vessels survive ok, large ones come apart), both vessels get locked together (distance won't change no matter what, engine burn stops affecting orbit) and this locked together orbit starts slowly moving away from Kerbin without changing shape. Stays circular but just moves away. If I wasn't accelerating before, and I do time acceleration, I get the same message, "cannot warp while under acceleration". Nigeth, is any of this similar to your buggy save?
