I know its been some time, but what did you do to make ir work?
I have the same problem, kongregate answer me with this:
It might be an issue with directory structure. Index.html is calling c2runtime.js and c2webappstart.js, which are in the KONGREGAME directory (the dev’s zip file) below the game directory, so index.html won’t find them.
I've also followed the tutotrial which is very simple, export game as kongregate, zip all files directly except index.html.
Upload index.html, click "I would like to add more files" and select de zip...
Thanks in advance,