I have a craft in about a 25km orbit around Bop right now, and it appears to be completely bugged out (note that only this ship is experiencing this bug, as far as I know). The orbit is changing completely on its own (it's burning radial out): with a dropping periapsis and increasing apoapsis very rapidly (a kilometer every 10-15 seconds). I've shut off all reaction wheels, RCS thrusters and engines and it it still occurs. The orbit doesn't change when the ship is out of focus, but if I try to dock with it, I find the ship moving on its own as well.
Furthermore, while I can still control RCS and engine thrust, I can't change the ship's direction at all (with SAS/RCS on or off): it's stuck facing the same direction regardless of the force I put on it. Using hyperedit to change the orbit doesn't help either.
I'm not sure of the steps to reproduce it because it's not happening with any other craft. I have around 50 mods installed, and here are the ones that may be problematic:
Action Groups Extended; AutomatedScienceSampler; B9 Part Switch; Better Burn Time; Community Resource Pack; DefaultActionGroups; DistantObjectEnhancement; Engine Lighting; Final Frontier; Fuel Tanks Plus; Hyperedit; Interstellar Fuel Switch; Kerbal Alarm Clock; KER; Kerbal Joint Reinforcement; Kerbodyne Plus; KerboKatzUtilities; Kopernicus; Mechjeb; Modular Rocket Systems; Module Manager; NearFutureConstruction; Outer Planets; SigmaBinary; Station Science; Stock Plugins; TAC Fuel Balancer; Tweakscale