I didn’t create the most flexible method of doing a portfolio in my themes, but what is happening is that with different sized thumbnails, it affects the rows below. So if an image is taller, it pushes the container down which then causes the next row to go as you see in your page. The only solution for this is to make sure your featured images for each portfolio item are the same size. It also helps for consistent layout and style too.
To create a layout that has different heights and sometimes even widths, the theme needs a masonry type script that realigns everything and floats them below each other perfectly.
If you make your thumbnails all the same size when applying them to the Featured Image, it should be ok…however, you might want to clear your browser cache just to make sure it’s not holding a previous version. If you are using a 4-column layout, your thumbnails should be 260×175 consistent throughout. You can use a different height if you want, but as long as every featured image is the same height and width.