This is because the font used by the default theme (Settings -> Style Configurator -> Select theme) is set to Courier New
and does not play well with Shift-JIS. If you change your font to something more JP friendly (e.g. MS ゴシック
), your file should display JP text correctly without having to change the preferences. You can also change to a different theme which uses a more JP friendly font. Themes where the font is not set (left blank) should work too.
Hope this solves your issue.