I have not confirmed your observations (I have all resonant antennas, so
it makes that check difficult).
However, I would think that the SWR reported by the KX3 would be the SWR
between the KX3 and the KXPA3 (which should be low) and the SWR reported
by the KXPA100 would be the SWR presented by the antenna feedline to the
KXPA100. Two different indications.