I'm using DS4 ver 2, on Dolphin 5.0. When playing Pokémon Colosseum and Pokémon XD, and I push the left analog stick straight down, my character moves straight up instead of down. If I'm slighty to the left or right, it moves as it should. In the Dolphin settings for the controller, everything is set as it should, and testing it with the moving red dot, nothing is abnormal. In the second game, you can also move your character with the c stick, and that works. The binds for the c stick are similar to the binds of the left stick, so it should be working. I didn't have this issue when I used a dualshock 3 controller.
The bindings for the control stick read "up", "down", "left", "right".
The bindings for the control stick read "up", "down", "left", "right".