I know this is an old thread, but i just found it while looking for something else.
We had same issues with kongregate (roughly even at same time as OP) and still happening very often.
You are doing nothing wrong. This issue is entirely on Kongregate side. We have been uploading 10 updates a day because of that, and spamming all possible support on kong (chat, other devs and all possible emails) for days. And finally some random guy from support explained what is going on on their side... Then few more guys were working with us to fix that... Which ultimately ends up on deleting our game entirely - by kong staff, and uploading our updated version again as a completely new game. Yup, we had over 1000 play after initial update, some comments, rating, positioning etc... All gone, new update equaled fresh start. Two days later we send update again... same thing happened. And then we gave up on Kongregate. Last game we published there only when we knew there are no very bad bugs in it.
On kongregate you have to upload index.html and zip file with all the rest. What is happening is that the new updated files from the zip are not replacing old files on their servers. Instead they might merge together making one big mess. We had situations where all text objects on the game was showing from new updated version, but graphic assets was still from old version of the game!
We didn't upload there anything in last couple of months, so maybe they finally fixed that idiocy (highly doubt it).
But just in case make sure your game is good as possible (regarding to bugs) before you upload it there!