Same problem here with the screwy warped graphical objects. I haven't touched the spy pengling yet (except for the blueprints) but I noticed as soon as i built my first snowfox and pad ever, when I left the hoverbike, it was halfway into the ground …
I found a post elsewhere on the net about this: If the ocean has disapeared it will come back after killing the player character. (on respawn it should be back to normal)