It happens to some guitars. Any brand and model (though more-so 6 in-line's than 3x3's I've noticed) is susceptible so don't feel like there is something wrong with it. As Pushead said, foam will fix it. I have an ESP Phoenix with the same issue and I just use electrical tape instead of foam. Just easier to deal with. If it's just one string the nut slot probably does need to be looked at.