Hey Matthew,
yes, I meant NavSetGroundReferenceHere... was writing from memory...sorry...
The only difference of NavSetAltitudeReferenceHere is that it only sets the - well - altitude and not also the horizontal position.
But I think I don't properly understand your issue. It sounded like you wanted to also update the waypoint altitudes so they have the same distance to the "ground" as defined in the flight plan.
Could you explain your problem more thoroughly again?
What altitude are you actually at when on the ground, what altitude does the aircraft report and what AGL is displayed in the GCS?
Remember that the AGL distance shown in the GCS is an approximation based on the rather coarse SRTM data. (Altitude over mean sea level reported by the aircraft, subtracted by the ground altitude at that location provided by SRTM data).
Also if you suspect a problem with the altitude estimation itself, please provide the paparazzI_version you are using together with the used ins subsystem (or even more conveniently a link to the airframe configuration file).
Cheers, Felix