chupecabres,
Well if your personal settings file is corrupted, the good news is that you can delete and remake it without much issue. You'll need to remake your custom controller settings and will lose your progress in your skill games (Which can both be a pain), but otherwise it won't affect your progress in modes like clubs, career, ultimate team, etc. That one's a relatively easy fix.
Do you have controller issues in other games too, and do you have another controller you can test this with? It's definitely odd behaviour, and it's not exactly the most common, so I'm wondering what could be happening in the background that causes this. Could you share a DxDiag? Hopefully there'll be something in there that points to the issue.