Yep, that's intentional. : )
Except, are you sure negatives were involved? This should only occur with X-stone, which is never negative unless something went VERY wrong.
Huh, I guess your browser auto-clears your cache or cookies. I can't prevent that, but I added a cheat code to restore "your" save file:
If you hold down the "E" and "Y" keys while you click New Game, the new file will have all levels completed up to 79.
Also, players can now press Esc to exit the white screen, instead of having to refresh the page.