This is a recorded message, please always provide the version of Geany, Glib and GTK (see lines near the top of Help->Debug Messages) and the operating system and version you are using.

WFM Geany 1.36 (git >= 4bceddb), en_AU.UTF-8 GTK 3.22.30, GLib 2.56.4 Linux Mint,

• create new file add "foo", there is no return at end of line
• ensure that the specified preference is unticked
• save file
• close file
• open file, there is no return on end of file

Note if you add a return Geany will not remove it and as @codebrainz noted there is a project specific version of the option which overrides the general option.

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