Could you make a Process Monitor log of what happens when you launch Opus for the first time?
That may reveal something unusual, either a folder that is being accessed or components being loaded into the process which might be causing the problem.
Do you see the same duplicate folders in File Explorer?
It may also be a result of the compatibility settings you've applied, since Opus filters that list differently for different versions of Windows.
Do you know which settings it has changed? It could be complicating things more than helping, since it's difficult to know what it has changed and whether those settings are still in effect, or how to clear them if they are.
Normally, any change you apply using it would still be in place after a reboot, so I'm not sure it's really fixing the problem if the problem comes back each day.
Some of the Microsoft extensions have had bugs in recent years as well. It might be worth disabling them as well, in case they're involved. Be sure to reboot afterwards, and re-enable things later if it didn't make a difference.