Did you enable the use of the GPSDO? You have to go to the Settings -> Reference menu and tell the instrument to use the reference.
Also, is your DUT being disciplined by the GPSDO?
We calibrate our devices to a GPSDO. If you just put our instrument on it, there might be minimal change (basically whatever drift there has been since we adjusted it in our facility). Once our instrument and the DUT is using the GPSDO, then I expect nominally ~0Hz offset.
