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As long as you exit out of Sigil completely, your settings should be saved for the next launch. Perhaps Sigil has no write access or permissions to your sigil.ini file?
You could try renaming your sigil.ini file and trying again, just in case it got corrupted. You also might try editing epub and saving the file but that should not be needed. Just really exiting Sigil should be enough unless you somehow have multiple instances of Sigil running.
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