Just that you should only need 2. I'd imagine the head has 4 out for front and rear speakers. The amp is wired for 1 L&R pair out and 1 sub out but has 4 inputs coming in?What's your thoughts?
I'd try removing CH3 and 4 inputs OR CH1 and 2 from the amp to see if that makes any difference AND/OR try the Input Mode switch to 2 CH instead of 4.
The sub output side should also have the LF switch activated with a filter of 150 or lower depending on your preference for the subs bass. Not sure why this hasn't already been set during install. I'd leave the other side (fronts) to off (full freq) looking at your speakers.
You may also need to tweak the Input Sensors (gain) for both after making these changes.
I'd also be tempted to do a full reset of the headunit to undo any changes you or the installers may have done to the sound.