Yeah, I had the same issue. Unfortunately, the only way I could get the game to run properly was if I downloaded the itch.io app and installed CoQ through there. I emailed the devs about it and they mentioned that the issue stems from permissions, for example that the account doesn't have enough permissions to the files for some reason, anti-virus is preventing the access, or the folder was unzipped into or from some sort of protected location like downloads. We weren't really able to come up with a solution, though.
But like I said, running the game through the itch app works fine. Same as with running it on steam.