Hey, once again sorry for the somewhat late reply.
Okay well, that's pretty much what I expected, that the controller technically works but the buttons are either jumbled or not detected.
I don't know what else to say really, if the manual is correct and GameMaker uses the same SDL library internally as you linked then I don't know why it doesn't work correctly.
We'll just have to see if it's fixed whenever I update my GameMaker version. (which will be "soon")
If it's not fixed with the update, then I don't know when/if it will be fixed but I will try to fix it at some point, it is currently not a high priority though.
Anyway, thanks for the feedback and I hope I'll get it fixed at some point.