Channel assignments which output Pixhawk 4 FC do not match what is programmed in my controller

I am experiencing issues with channel assignments on the output side of the Pixhawk 4 FC (they do not align with my remote control settings). Everything works as it should when everything is connected to the receiver only (nothing going to the FC). I am using qgroundcontrol, and all of the channels appear to match that of my remote control. I am attaching a picture of my setup for reference. Please note that this is a bench test setup, but has a layout very similar to how it is setup in the aircraft. Any advice would be much appreciated.