Hai provato a disabilitare il suffisso URL? O ci tieni proprio che gli URL finiscano con.html? Per comodità ti posto la sezione SEF del mio .htaccess:
## Begin - Joomla! core SEF Section.
#
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
#
# If the requested path and file is not /index.php and the request
# has not already been internally rewritten to the index.php script
RewriteCond %{REQUEST_URI} !^/index\.php
# and the request is for something within the component folder,
# or for the site root, or for an extensionless URL, or the
# requested URL ends with one of the listed extensions
RewriteCond %{REQUEST_URI} /component/|(/[^.]*|\.(php|html?|feed|pdf|vcf|raw))$ [NC]
# and the requested path and file doesn't directly match a physical file
RewriteCond %{REQUEST_FILENAME} !-f
# and the requested path and file doesn't directly match a physical folder
RewriteCond %{REQUEST_FILENAME} !-d
# internally rewrite the request to the index.php script
RewriteRule .* index.php [L]
#
## End - Joomla! core SEF Section.
L.