Hello. I have the same problem — trying to fix this at wheresmynotes.com which is a fresh WP install.

All I have in my .htaccess is the following. Is there a way to get the plugin to correct the file by itself? What could be the problem?
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ – [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
Thank you!