in the webassist/plugins/catalog/css/products_detail.css file, the following css is causing the qty box to shift to the right.
.productDetailWrapper .addToCart form label {
padding:6px 3px 0 3px;
width:140px;
text-align:right;
display:inline-block;
margin:0;
white-space:normal;
height:auto;
}
change the text align to left and the width to move the qty box to the left.