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Make sure you have fully exited from Sigil and that Sigil is not running at all (use Sigil Quit instead of just closing the Window). Then try renaming the entire ini file to force Sigil to create a new one.
If you are still having an issue after that, my guess is Apple has cached the program window state in some way. So shutdown your machine and make sure to *uncheck* the box that says reopen applications.
Then repeat renaming the ini file on reboot before starting up Sigil.
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