A control system and method for controlling two motors determining the azimuthal and circumferential position of a magnetron rotating about the central axis of the sputter chamber in back of its target sputtering and capable of a nearly arbitrary scan path, e.g., with a planetary gear mechanism. A system controller periodically sends commands to the motion controller which closely controls the motors. Each command includes a command ticket, which may be one of several values. The motion controller accepts only commands having a command ticket of a different value from the immediately preceding command. One command selects a scan profile stored in the motion controller, which calculates motor signals from the selected profile. Another command instructs a dynamic homing command which interrogates sensors of the position of two rotating arms to determine if the arms in the expected positions. If not, the arms are rehomed.