WOW, yes, your problem is almost certainly Flatpak-related. I’m surprised you even got as far as you did. Flatpak is often great but does not tend to play well with applications that need less common capabilities.

I’d recommend installing VMM in a different way if that’s an option for you; I expect that will likely make your problem go away.

Well, what are the permissions of /run/usr/1000/doc/c0a3c3fc and what user are you running VMM as?