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No, in the latest releases you can set epub to launch with Sigil or drag and drop an epub on the Sigil icon and it will happily open just that epub with no empty MainWindow hanging around.
Did you do the entire sequence like I asked:
- erase Sigil from app cache
- remove or rename Sigil ini file
- restart your machine without the reopen windows box checked
After restart up Sigil and rearrange windows the way you like and save and exit to write the settings to the ini file.
If that does not fix the issue, then try changing your screen resolution to see if that impacts the issue.
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