The problem is that the box background filled by createPattern also is moving.
Actually your problem is that the background is not moving - it is static, while you are drawing your rectangle to different positions.
How to avoid that?
The pattern will always be drawn at the coordinate origin, whose actual position is defined by the current transformation. In future you will be able to transform the pattern itself with the setTransform method, but since that currently is not implemented anywhere you instead will have to change the global transformation matrix.
In your case it means, that instead of drawing your rectangle at x/y, you translate the whole context to x/y and draw your rectangle at 0/0 then:
ctx.fillStyle=pattern;
ctx.save();
ctx.translate(boxes[i].x - left , boxes[i].y);
ctx.fillRect(0, 0, boxes[i].width, boxes[i].height);
ctx.restore();
(updated demo)