Your sigil.ini is missing the entire preserve entities section as well. All of your other ini files are fine. Have you ever used the Sigil Preferences Preserve Entities settings at all?
If not your ini files are fine and then we are back to what BetterRed suggested that something on your Windows machine is causing havoc for Sigil. Please try booting your machine into safe mode and then run Sigil for a while to see if that changes anything.
Thanks!
KevinH
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