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Specifically, this seems to apply only to preferences relating to the “Notification Area.” I want to “Show qBittorrent in notification area,” and “Close qBittorrent to notification area.” For the most part these settings work as I want them to. However, if I reboot, or log out and in again, they stop working.

• qBittorrent is set as a startup program.
• If I open the preferences dialogue on startup, “Show qBittorrent in notification area” is greyed out, along with its contingent options.
• If I close qBittorrent and open it again, the options are available, and if selected will work normally until the next reboot.
• It is possible FileZilla is also exhibiting this behavior. Whenever I perform an upload and hit the “Target file already exists” dialogue, I select “Overwrite if different size or source newer,” and tick “Always use this action.” It seems like that second checkbox ought to mean I don't need to see this dialogue every time, but perhaps I don't understand this particular application adequately? More research required.

I am sorry to say, this issue appears to have resolved itself. I did not update the software, and I had not tinkered with the issue in some time. I do not know why it resolved itself.