I had just started to second round of the game when the badges were uploaded, and apparently that doesn't count for the badges. You saying I now need to beat challenge mode if I want the badges? :/
Don't really appreciate getting kicked to the Kong home screen every couple minutes. Can you make sure that the game actually works well before making a contest around it, Kongregate?
You can always use the Reset Game button. You will get percentage bonus to speed up the second playthrough.