The In Motion bit goes high anytime the master is commanding motion. Each master has an In Motion bit, which can be found in the Master Flags, Primary Master Flags.
Jogging does not trigger the In Motion bit. This is because a jog move is not created by the master profile. If the application requires jogging, then the Jog Active bit (Axis Flags, Primary Axis Flags) should be used.
In order to monitor whether motor is moving, for both discrete and jog moves, the In Motion bit and the Jog Active bit should be used.