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What version of Sigil? What O.S.?
(5.11.2 is the Qt5 version, not a Sigil version number)
I don't have any trouble with the latest Sigil using entities. Perhaps your Sigil.ini file is corrupt. Back it up, delete it (or rename it) and relaunch Sigil so it generates a new one. See if that fixes the issue.
You really shouldn't have an empty Preserve Entities list. The bare minimum is   (for EPUB3) and (for EPUB2). That's why is added by default. Bad things can happen if you run without one or the other (though I've never encountered the issues you're describing).
The next versions of Sigil will be able to run without any entries in the Preserve Entities list.
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