I encountered this too. The solution for me was: (always backup your site before trying any solution)
I renamed .htaccess file to .htaccess_old and then went to WP>Settings>Permalinks and click the SAVE button. A new .htaccess file was written however it was the default clean install version; no security settings.
I went to the iThemes security controls and tried re-saving. Nothing written to .htacess.
When I deactivated and deleted the plugin and then reinstalled it all of my settings were still in place and after saving – the .htacess file was updated with the iThemes settings.
The .htaccess_old file could then be deleted.
As always. Write down your settings and backup your site before trying any solution.