I had an issue where my right stick would not turn left or right, only up and down, I couldn't find an answer online so I figured I would post the solution here for others having this issue.
For whatever reason when you try to map the analog sticks using the SDL protocol the right stick will only go up and down, while the right and left map to the left analog stick. I don't know what causes this, but I did figure out how to fix it. Setup your controller buttons and sticks as you normally would, then at the top right type a name in and save it. Now close Dolphin and go to your "Documents\Dolphin Emulator\Config\Profiles\GCPad" and find the file named after the profile name you just saved. Open the file using NotePad or any text editor, half way down you'll find the "C-Stick/Left and C-Stick/Right" most likely set to (Axis 0 - and Axis 0 +). To fix the issue simply replace the 0 with 3 for both lines, make sure its the C-Stick, not the Main Stick. Now save, close, and reopen Dolphin, go back to controller config and at the top right click the drag down menu and select the profile and click load. You'll see now that both Axis have changed from 0 to 3 and that's it! I think it should be universal but if this didn't work maybe try Axis 2 or any Axis between 0 and 4 that isn't already being used in the mapping elsewhere, hope this helps!
For whatever reason when you try to map the analog sticks using the SDL protocol the right stick will only go up and down, while the right and left map to the left analog stick. I don't know what causes this, but I did figure out how to fix it. Setup your controller buttons and sticks as you normally would, then at the top right type a name in and save it. Now close Dolphin and go to your "Documents\Dolphin Emulator\Config\Profiles\GCPad" and find the file named after the profile name you just saved. Open the file using NotePad or any text editor, half way down you'll find the "C-Stick/Left and C-Stick/Right" most likely set to (Axis 0 - and Axis 0 +). To fix the issue simply replace the 0 with 3 for both lines, make sure its the C-Stick, not the Main Stick. Now save, close, and reopen Dolphin, go back to controller config and at the top right click the drag down menu and select the profile and click load. You'll see now that both Axis have changed from 0 to 3 and that's it! I think it should be universal but if this didn't work maybe try Axis 2 or any Axis between 0 and 4 that isn't already being used in the mapping elsewhere, hope this helps!