Yup... this happened to me about 3 months ago, and unfortunately for me it was my controller was "dying". I have no clue why controllers now days are so cheap (yet you spend out the butt for them...) and hardly last. Yet my Gamecube controller I had from when I first got my Gamecube back when they first came out is and still works in pristine condition. /sigh

Anywhoozles, rant aside for me and 99% most likely for you it's time to get a new controller, the minute I had a new controller all problems like that stopped and hasn't came back since.