What do you mean by "simply reversed the channels"?

I reversed left and right servo leads (Rt to Aux- Lt to Aile) on receiver and also tried programming the DX6i aileron reversing. The ailerons worked either backwards or they both moved up & down together when I engaged the FLAP switch.

They work okay with the DX6 transmitter but not with the DX6i. I'm using an AR6100 receiver. I have other issues with the DX6 transmitter so I don't use it anymore.