It appears to happen only when the backups are running. I have noticed that even if the window doesn't disappear, it can still take quite a few seconds to show up while everything else is immediately there.
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On desktop 1 I have a browser window and FreeFileSync (backing up to an external USB drive) running while I'm working on desktop 2. After some time I go back to desktop 1. The browser window is still there but FFS has gone. It is still running because I can see the external drive still working and t...