I'm not a GCS programmer, but it may be that simply entering the custom vehicle setup has changed the vehicle from e.g. XQuad to Custom.
One way to debug this would be to export settings to 1.uav, enter the custom dialog, leave the custom dialog, save settings, export settings to 2.uav, compare 1.uav to 2.uav. If there truly is no difference, it should probably be considered a bug.