If you look at this fiddle and 
- while observing the numbers in your divs - you see that the next masonry element up (the red element 5) can not possibly fit in the white square as it must come after element 4; so where it must end up means, that, with only three rows fitting, you'll get a white gap. Maybe you can use Isotope's shuffle and reLayout methods and sacrifice ordering your elements in a strict order?
