I have my aircraft set up like this

1 = Left Aileron
2 = Elevator
3 = Airbrake
4 = Rudder
5 = Left Flap
6 = Right Flap
7 = Right Aileron

You are correct about both sides being negative when you change the left side on the differential menu.

It shouldn't matter what value I set the differential to, on CH1, CH5 should not reverse due to a value in CH1's differential setting.

The flaps should always move together with the flap trim, regardless of the aileron differential. There is no aileron > flap mix enabled on my radio either. Actually differential is the only thing that needs to be changed to get this to happen.

Can you try your test again AnnMarie?

Thanks,
Steve