Yes it is about Top-level folders.
Sometimes all the folders disappear, sometimes only few.
This is happening to me on my desktop and on my laptop, both with Windows 10.
Sounds like something is preventing your system registry from retaining the info that the Favorites uses to preserve/restore that information. For a problem like this, I suggest contacting our support folks at:
By email: support@camerabits.com
By phone: +1 503.547.2888
Hours: Mon-Fri, 9:00am-5:00pm [PST/PDT]