nothaseo
Perhaps it is because you've archived the entire game folder into zip.
Correct way to submit a HTML5 game on Newgrounds is to archive all the game files inside game folder, not the game folder itself. Just select all the files and folders inside the game folder and archive them into sole zip so when you look into zip file you will see not the game folder but the files and folders that usually are inside the game folder.
Sorry for my inability to explain in proper English, I ain't into it that much.