I'll second the "two finger" technique recommendation, it might help, if only to tell your brain it's different from the video game console.

Beyond that, try a little "dry flying" at home. Set up your plane on the floor in front of the TV some night, grab the TX and mess around with the controls and see just how slowly you can move the stick smoothly from the center to full travel and back while watching the control surface. Do one control (ailerons for example), then do another (elevator). Then do the movements you'd expect in a turn, roll in (say, left aileron), center ailerons, apply and hold a little up elevator, center elevator, roll smoothly out. If you do it smooth while doing something like watching TV, you came help make it more automatic. Then you'll just have to get those movements to work with what's going on in the air.
It sounds silly, but it might help reprogram your fingers.

Another thing, try reducing the control throws on your trainer.