For accurate calibration of Fourier transform spectrometers we must constrain or resample the interferogram data to an invariant sampling comb. This can become challenging when instrument self-emission is significant and beam splitter absorption is present. The originally-sampled interferogram center-burst position can move due not only to sampling comb changes, but also to an interaction between the strength of an external target and the so-called anomalous phase (the two ports of the interferometer contribute center-bursts at different locations, and the relative weighting of the two ports varies with the strength of the external target). We present a model of the anomalous phase to enable partitioning of changes in observed center-burst location between sampling comb changes and anomalous phase effects.