I've been seeing that as well. Does not happen when outside of the js1k frame (http://johan-nordberg.com/2048/).

I think it is some hisenbug related to that js1k loads all entries by injecting the script in a iframes src attribute.

EDIT: clicking anywhere to focus the iframe makes it stop

Yep. Also the tiles sometimes initially appear well off from where they actually are, which is an additional disorientation.