A system and method for holding position of a mover in an independent cart system includes receiving a current feedback signal corresponding to a current present in at least one coil for a linear drive system in the independent cart system. A motion command for the mover is received, where the motion command defines a desired position along a track of the independent cart system to which the mover is to travel. An electromagnetic pinning control mode is disabled while controlling operation of the at least one mover to the desired position and enabled when the at least one mover is at the desired position.