After upgrading to v5, I got to work sorting my Rules into Folder Groups. I used the search field to narrow down my folders, and at times when dragging the folders that matched the search results to the desired Folder Group, my screen would go black. This happened repeatedly.
The computer was still running, and a keyboard tap eventually brought back the screen, which led me to hypothesize that maybe Hazel was running some disabled rule (or one that just shouldn't be triggered) that put the display to sleep.
Also during this process, Hazel would at times just come unresponsive. No beachball, but it was "frozen". Even more oddly, after a Force Quit, I went to relaunch it from the Recent Applications folder in my Dock, and got a strange message along the lines of "The application Hazel is not current running" or something similar.
Now, I am seeing all my Folder Groups are gone. All the folders are still there (I think), but the Folder Groups they were in are not. They appear to be in the order they were in when in the Folder Groups.