I am having this same issue, and it's driving me f***ing insane. It doesn't happen on every craft though. At first I figured it had to do with weight or maybe odd size/length, but I have had issues with this problem randomly on craft of a variety of sizes/weights. Currently I'm trying to piece together a space station and I keep having to redesign stuff over and over cause I will get into orbit with a piece and then MechJeb just spins and spins chasing the maneuver node never "completing" the burn, even though the DeltaV needed will get as low as 0.1m/s. Disabling and immediately re-enabling autopilot can resolve the issue, but during rendezvous it will cause you to change orbits at incorrect times and you'll never meet up with your target.
