A motor controller is provided that executes a commutation routine in one of a plurality of operating modes to regulate current provided to drive coils in a linear motion system. The motor controller generated currents for each of the drive coils in a first operating mode to minimize the copper losses in the drive coils, in a second operating mode to maximize the force applied to the mover, in a third operating mode to provide balanced currents between the drive coils, and in a fourth operating mode to provide currents according to a selected operating point that combines characteristics of the first three operating points. The motor controller may also monitor each of the drive coils for saturation and redistribute at least a portion of the current required to control operation of the mover to the other drive coils when one of the drive coils is saturated.