Do you have some, as detected with a slow roll? After the mechanical runout is thoroughly verified as well.
Can you shift the prox probes axially to a "better" surface?
It can be caused by actual magnetism, or varying material properties within the shaft, as might result from situations like uneven chrome thickness on a repaired shaft.
Some turbo machinery repair shops offer demagnetizing, burnishing, and probably other processes to to reduce it. Seems like modern software ought to be able to compensate for it, after detecting and mapping with a slow roll.