I had queued up building a few energy storages when my commander suddenly vanished, zooming out and looking for him I could see his unit representation icon but not the unit itself. Like before, recorded and uploaded the act of it being underground - it emerges out of the sea by the end of the clip. Link: http://www.youtube.com/watch?v=EJEPVyhY7Xo
Known issue. Avoiding Water and Ravines is the only "workaround" at the moment. We're waiting on a Pathfinding update which should come soon.
More specifically, for this issue, if the commander (or any unit) has something built on top of them they fall through the planet surface. The work around for this is to try to make sure units don't build stuff on their heads.