In this paper we show an up-to-now unexplained source of offset drift affecting the fundamental mode orthogonal fluxgate. After a sudden change or removal of the magnetic field, we observe an offset transient which lasts units to hundreds of seconds. We exclude the thermal origin of such transient as well as the electric origin in the pick-up coil resonance circuit or sensing amplifiers. We prove that this transient has magnetic origin, since it depends on both the amplitude and the duration of the pulse of magnetic field applied to the sensor which can be expressed as magnetic energy. We conclude that operating the fundamental mode orthogonal fluxgate in a closed feedback-loop is useful by suppressing this transient behavior by keeping the core in a (almost) zero field, however when switching the magnetometer sensor on/off, this transient has to be taken into account.