You can set the EDID of the nBox to match the native resolution of the projector, in order to make the IG generate the correct resolution.
This is done by navigating to: Projection Theatre > All nBox Processors > nBox processor X > Input Port 1 in the Theater Explorer.
At the bottom of the Properties dialogue scroll to the right on the tabs and find the EDID tab. (see attached picture)
Then Press Load EDID and navigate to the EDID files (see attached picture)
And select the EDID file with the correct resolution.
Repeat for each nBox processor in the system.
Save the CVD file.
Restart the system and the resolution should now match the selected EDID.