You may try replacing the complete WP rule-set with this one:
# BEGIN WordPress
RewriteEngine On
RewriteBase /
RewriteRule ^index.php$ - [L]
# Include in the next line all folders to exclude
RewriteCond %{REQUEST_URI} !(folder1|folder2|folder3) [NC]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
# END WordPress