There seems to be an issue with the pannning of the GRO's internal mixer. I noticed this when I was trying to replicate an organ with remote divisions in different parts of a church.
So, use the GRO's Mix page pan control for the Hauptwerk, say, to move the sound to the left. Now save the project and re-open it. On checking the pan control, it will be exactly as it was before the save, panned to the left. However, the mixer internally has not applied this panning and the sound is at the normal location for that manual. Now touch one of the handles of the pan control and move it very slightly. The pan is now applied again and the sound will jump to the left.