Ok, this one is a bit complicated, but here it is:
Generally when a prop is designed in the modeling to spin in one direction and a user or re-modeler edits the aircraft.cfg propeller section for counter rotation, the prop will spin in the counterclockwise direction through shutdown until it reaches a random RPM moment at which in begins to spin in its originally designed clockwise direction. This is rare, but as you've witnessed it does happen. Check the aircraft.cfg for CCW rotation and revert it back to CW.
The other problem with "continued rotation" long after shutdown suggests erroneous data somewhere in the prop sections of the *.air file, i.e. 510, 511 and 512. Using AirEd, the quickest remedy is to find another model with similar prop dimensions and blade count and copy its sections 510, 511 , and 512 to paste/overwrite into the same sections of the offending model.