OK, I checked and my controllers are not duplicated. In fact, I had deleted the keyboard commands for the axis controllers back when I set this up long ago. I had even deleted the duplicated axis controllers in the "Ka-50 Game" drop down so they're not duplicated there.
The thing that is bothering me is that all 3 controllers show up in their separate columns, but it shows "joy_x" and "joy_y" under the throttle column for my mini-stick that I use for the shval but it also show the same name for the axis under the combatstick for the x/y axis for pitch and roll. They are different controllers so I would think there's not a conflict here but are you stating something different?
I was going to take a screen shot but I can't find the file. Do you know what file the screen shots are stored in?