Hey Leethal,
Have you tried monitoring the levels in SmartPropoPlus? This would be the first thing i'd check; is the drift caused by a controller or something to do with the way the PPM is being interpreted by SmartPropoPlus.
One thing you could potentially do is modify the rudder channel on the Spektrum DX6 to be slightly offset?
The only other thought I have is possibly look into adjusting of output in the controller? I've read on previous forums about PPM input jittering. This youtube video is one place I've watched to correct jitter on my Turnigy 9x.