Hi,
It is because you use the following custom CSS:
[html].asp_isotopic_item {
padding: 15px !important;
width: 33.3333% !important;
position: static !important;
height: auto !important;
background-image: none !important;
background-color: transparent !important;
}[/html]
This changes the item width to 33% and the calculation for the isotope rows count uses the value that is defined under the plugin Theme Options -> Isotopic results panel: https://i.imgur.com/YQLvDP3.png
Since this is a different value, the calculation comes out incorrect.
Instead of forcing the width, I recommend using a higher width value, like 400px or 500px on the back-end, and the isotope script will try to maintain that, with the correct rows count.