You have no notification that the site settings has been saved. I suppose that you are using a linux version of Publii and you have no libsecret package, which is required by Publii to safely store passwords. Please install the missing package: https://github.com/atom/node-keytar#on-linux and please try again.
I will check what can be a reason of the silent fall back in this case to avoid such no error cases in the future 🙂
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