Hmmm, well there are a few key things that can mess up the export for itch.
First, make sure you're hitting the "Export Project" button below and NOT the "Export PCK/Zip" button
Then you can save the files wherever you want, but you HAVE to save it as "index.html" (see below)
That should leave you with a list of files like you see below (everything in the red box)
You can cut/paste all those files into a Zipped folder (The name of the zipped folder doesn't matter) and THAT folder is what you upload to itch.
I apologize if you already knew some/all of the above, I don't mean to insult your intelligence :)
Just trying to track down what's messing up the export.
As a side note, I don't believe, in this jam, we can upload any new files during the voting period.