Sorry for the delayed response. If your'e changing the URL for the Like button, the count will reset to 0. So, we'd recommend standardizing on just one URL for your Like's.
From what I understand, you want 2 different comment boxes on each page, correct? You should be able to manually add the tag for each URL on the page like:
{JFBCComments href=http://site.com/en/link-to-page/ width=200}{JFBCComments href=http://site.com/fr/link-to-page/ width=200}
That should make 2 side-by-side comment boxes for 2 different URLs. I agree it's not going to be fun to do that on a lot of pages, but not sure a better way to do it. If your pages have 2 different languages and are on different URLs, Google, Facebook, and everything else will see them as separate. It makes sense that they'd each get their own individual comment box.
Hope that helps, but if you still can't get it, let us know.
Alex