Docking issue in 0.18. After separating a craft, reconnecting the craft causes Mechjeb to put the craft into an uncontrollable spin when attempting any tasks.

Attempting to reconnect a craft to itself after separation causes an uncontrollable spin.

For example, in an Apollo style mission, after launch, kerbin orbit and the transfer burn to the mun the next step is having the command module undock, turn 180 and attach to the lander(1) to transfer crew before circularizing around the moon, then separating once more (2) for the landers descent to the surface.

Example 1. The MechJeb Unit (AR202) is on the lander section. After separation and re-docking(1) with the lander, Mechjeb ceases to function properly, any input (Smart A.S.S, Landing AP, Ascent AP etc.) causes Mechjeb to perform an uncontrollable spin.

Example 2. MechJeb (1m) on command pod, Mechjeb (AR202) on lander. MechJeb Continues to function after docking maneuver (1). Upon separation in preparation for descent (2) MechJeb on the lander ceases to function properly, with any input (Smart A.S.S, Landing AP, Ascent AP etc.) causing Mechjeb to perform an uncontrollable spin. Command Module MechJeb Remains functional.

Both modules are powered at all times. Lander has a probe part built in for unmanned control.