Mega Man X4 mixes up Xbox 360 controller buttons

[crashgordon94]

As the topic suggests I have a pretty simple setup for this specific game, just setting most of the buttons for individual keys, but when I go into the game itself and I press the buttons on my controller, they do the wrong thing, usually as if I was pressing multiple at once!
I press the keys on the keyboard itself and they do the right thing but pressing the button I assigned to do that key doesn't work, as explained previously, even though it's doing it right in the Xpadder window, I don't normally have this problem with anything else I use Xpadder for and running it as an administrator doesn't seem to do anything.

Can anyone help?