Very odd... The binaries on both sites should be identical (I upload the same version to each site). I will be putting up a new version later today, though, so lets check back and see if that makes an difference.
Now, that said, even though the binaries are exactly the same the version on Kong does more. This is because the game tries to make calls into javascript to post data into the kong stats tables. It does then when you visit the scores posting dialog in the game. When running at KnuckleCracker, these calls do nothing because there are not such javascript calls on the web page. When running on Kong, the javascript calls exist and the game makes them. After that, what happens is dependent on whatever Kong does in those javascript calls. They really should be little more than making a request back to kong to submit some data, though.