I’m not very familiar with PowerShell, but in the Linux command line shell, I’ve noticed that if you give a path for compression, it will include all folders inside, so your archive would include the folders “web” and “AKnightEternal”.
Could you try before the line with “Compress-Archive” to do:
cd web\AKnightEternal
And then on the “Compress-Archive” change the “-Path” to:
Compress-Archive -Path “.” -DestinationPath AKE-web-$timestamp.zip
This is just a guess, to see if that would work. You did mention that if you view both archives from the windows explorer they are both the same, but do they contain the same amount of folders? If that’s the issue, it would explain why Itch can’t detect the “index.html” file (since it’s not in the root folder) and it also explains why they have slightly different size.
Hope that was the issue.