If you have troubles since the update to WordPress 4.5 please read this post before opening a new thread.
1) The issue is caused by an image ( http://kirindesigngr.com/wp-content/uploads/2013/11/SilverberryKitchenLogoWhite_Full.png ) which is not resized by wordpress because the original image height (174px) does not exceed (or equal) the defined thumbnail height of 179px. The 4px height difference causes the uneven grid.
2) The related portfolio entries do not support a greyscale overlay (i.e. compare the demo page: http://www.kriesi.at/themes/choices/portfolio-item/happy-holidays/ which also shows colored thumbnails).
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