Its odd, it does it when I am playing it in my car usually, when the screen is off and it is down.
I thought it had something to do with copying it to the memory card by mounting it and dragging over, so I installed and used doubleTwist, which seems to queue the transfer like an ipod does in order to send the tracks slowly no matter how many you add. It helped reduce the amount of skipping, but it still happened after, particularly with Armin Van Buuren tracks and Cut Copy, but these tracks are fine on any other device.