Has the fueling position syntax changed?
That one always indicated the position from ground. However, the green bar in the 3d window displayed the height relative to the airplane reference point, so it was a bit confusing, since they didn't match (it was just a display issue) so, we changed this in an update, but it happened in December, now both editors show the same height, which is relative to the ground.
Note that, although the height displayed in the editor is relative to the ground, the height USED by GSX (which is stored in the GSX.CFG file) is relative to the airplane center, otherwise you wouldn't be able to create a reliable configuration, because it would keep changing depending on your load.
So, what you cannot do, is to use an height value you read on the GSX.CFG file, and put it back in the editor, because they mean different things but, as long as you only use the editor, all the heights displayed are coherent.