Comparison of wrong folders > "significant difference"

[Heineken]

I defined a sync job comprising 13 Folders. Run from the GUI - works as expected.

Running in background brings up the message "significant difference" between Folder A/A and B/A (Same folder name local and remote). The folders, however, are identical, having been synced before in foreground.

After carelessly having clicked away this message, the warning displayed two different folders, which made me look again and realize that a lot have files have been deleted (fortunately just on one client).

I wanted to try out if the troublemaker is always the same folder or the sam item in the sync list, so I moved said folder to the top of the list. It seems to have solved the problem.
[EDIT:] Problem still persists.

[Heineken]

Great support here...not.
My problem got worse. Now large numbers of my files are deleted on random days without the warning described above, after trouble with the VPN connection to the remote drive (this happens on other days, usually doesn't cause mass deletion).
This causes more work than it saves. Sadly, I'll have to look for another syncing solution.
I'd like to take my premature donation back.

[Zenju]

It's not clear what the problem actually is. Is it that some folder is reported by FFS as missing, but should not be? Can you give a more precise error description including expectation what should happen? Maybe a few screesnhots could visualize the details.