I'll try to clarify.... You are absolutely correct that LEGO drops their sets into the boxes vertically, but the flaps are always on the top and bottom. This way the flutes (those little wavy pieces in the middle) always stay vertical. You get the most edge crush strength when the flutes are vertical. The way you've stacked your packing boxes, all of the flutes are horizontal which means the LEGO boxes inside are carrying a fair bit of the load from the second and third rows.
Scroll down to the Stacking Strength section ... http://en.wikipedia.org/wiki/Corrugated_box_design
And yes I realize that LEGO uses the same flat boxes for shipping (unless you get the original LEGO shipping box) but at that point they are generally assuming the consumer and shipper aren't (edit, oops) stacking them on their sides. And if you consider post offices and delivery trucks, they usually have shelves so that boxes aren't stacked more than 2 high. (hah, at least they shouldn't)
Here are some pictures that hopefully help...
Flutes in the cardboard provide vertical strength..
Flutes run the same around all sides of a box..
Stacking on the side doesn't get strength from the flutes..
Stacking top/bottom does because the sides provide crush strength to the next row.
So the ultimate strength is in fact stacking boxes of the same size perfectly on top of each other, flaps to the top and bottom. Having said that, you can't stack forever. Crush strength of the bottom row is the only important one to consider. Criss-crossing rows is best when the cardboard has no flutes (like regular LEGO boxes).