Autopilot Orientation - Not working Correctly

I’m running the pixhawk 2.4.8 with PX4 version 1.13.0
The FC is setup rolled 180 and yaw +45 degrees for best fit. So the orientation has been set as "ROTATION_ROLL_180_YAW_45 using GCS version 4.1.5

However when I roll with the transmitter the roll is about the axis of the flight controller arrow not the correct axis of the quad. Pitch is also acting relative to the FC and not the quad.
Is this an issue in the firmware?