Cool trick. I'll watch it a few more times and try to figure it out before resorting to the Wiki answer.
It's the way the blocks are cut that it forces a square out when it is rearranged. That's what I think it is. The misalignment crowds out the block.
Why does he cut the video at 0:30 and 2:20 as he's taking it out of the framed box? All he does with the video edit is ffwd by maybe a couple seconds at most...seems like he's up to something there as well. In the end, he's probably using the method shown by wiki given how poorly the blocks later align, but I found it odd he would fast forward the video at those two places of them all...
Probably like this one where the size is changed while the squares are moving, although this is the reverse. http://www.geeksaresexy.net/wp-content/uploads/2013/03/neverendingchocolateanswer.gif
It appears that when all the boxes lie in the container, they appear reasonably uniform. He then cuts the video and re-arranges the position of the pieces so that when the pieces are removed from the box and rearranged on the table, the boxes are no longer reasonably uniform - one row of boxes is distorted.
Changed a middle piece going into 3 square removal (pic 1)...replaced it going back (pic 2). not math but sleight of hand. Image Unavailable, Please Login Image Unavailable, Please Login