I don't actually generate the ZIP file on Itch.io side; I use something called the itch.io Butler (https://itch.io/docs/butler/) which then does the upload in a delta-patch manner, similar to Steam's contentuploader.
It IS strange that it's only a problem on Itch.io, though. Let me poke the itch.io team, and see if they've got any suggestions. What's the error message?