When I select the four vertices on the top face [which also selects the edges and face], then I use 's' for scale, the 4 top vertices either move directly towards the center all at once or directly outwards all at once. But yours doesn't react that way EXCEPT at 2:52 when it mimics the only change to the mesh I get. Am I missing something?
Same issue for me. I tried removing doubles, but still get a uniformed scaling.