It's because by default bootstrap columns have a left hand margin, but this is removed for the first span div within the row:
.row-fluid [class*="span"]:first-child {
margin-left: 0;
}
So the left hand margin is removed in the first span3 div but none of the others. One solution would be to keep the left hand margin in the first span, see http://jsfiddle.net/panchroma/QePYB/