A 3D measurement device sends a beam of light to a point on an object, receives the reflected light, and determines a distance and two angles to the point, one of the angles measured by an angular encoder, which includes a disk having incremental marks and an index mark. Light from the 3D device is rotated to reflect light from a reference reflector to produce a first synchronization signal. A first difference angle is determined based on counts of the incremental marks and on the first synchronization signal. Light from the 3D device is rotated to reflect light from the reference reflector to produce a second synchronization signal. A second difference angle is determined based on counts of the incremental marks and on the second synchronization signal. The reference correction value of the index mark is determined based on the first and second difference angles.