In the next version of 3DSController there is support for customisable controls which should fix your problem.i want use my 3ds in dolphin but i have a lot of problem with the input. the most of the button have the same input in this emulator. i tested the 3ds with visualboy advance and with snes9x and there worked well. how i can solve the problem?
To all those who can't get this working, the next version allows you to change the port that is used, hopefully this will fix it, if not, then I don't know what the problem is.