He normally extracts his games into the downloads folder (iirc, I might be wrong), and then he adds the games into his steam library as "non-steam games". It's either the non-steam thing's fault, or the download folder fault, it might even be both of those.
Very likely, so, yes. For one, the game should be launched directly, either from Itch itself, or from its application. And normally, when you download things from Itch (if you're using the application of Itch) then a dedicated folder is created for the games.
Considering you said he put it in his downloads folder, I would assume he downloaded the file more directly. He should extract it to a folder that isn't just downloads for most stability. Perhaps its own dedicated folder, he can label however. It wouldn't be the first time I've seen someone have this problem because the game wasn't in its own, dedicated place.
Try that, and see what happens.