After starting the game, change the "Jump: both" setting to "button 1" or "button 2" and try again.
That would make sense for a controller with just 2 buttons, but most controllers nowadays have 4. Anyway, I'ts just a matter of getting used to it, not a big deal. The stick having the vertical axis inverted is a bigger problem. The first time I run the game I tried to change the settings but I couldn't, I move up the stick and pressed up in the crosspad with no luck, so I just started to play. That's because the crosspad doesn't work and the stick is inverted, I have to move it down to go up in the settings. And the same ingame, move it up to crouch.