Invalid URL Aliases in Drupal Nested Sites/Subsites - Main 404
Option 1 - base_url
Maybe you want to do some experiments to see if setting the $base_url in your settings.php somehow helps.
Option 2 - RewriteRule
It might be worth trying to further enhance your .htaccess file, by adding a line after the line containing RewriteBase, which looks like so:
RewriteRule . index.php [L]

For more details on the above line, refer to the (accepted) answer in this question on StackOverflow.