Paolo,
The FB Comments box should display to all users and all comments should be visible to all of them. The only time that comments become hidden to the public is if you (the admin) mark them as hidden. That will hide the comment from all users who are *not* friends with the user that posted them.
So, really not sure why the comment box would be behaving how you describe. Can you post a link to a page with the issues and we'll gladly look into it further to see if there's an issue on the page or something else that may be causing the problem.
Finally, the only other thing to check that I can think of is to make sure that all the user's are posting to the same URL. Basically, check that the page with the comments box isn't being accessed in different ways, like:
yoursite.com/article-with-comments.html
www.yoursite.com/article-with-comments.html
yoursite.com/index.php?option=com_content&view=article&id=12
That can cause problems, but not always. JFBConnect tries to fix the multiple-URLs issue, but sometimes there are some issues still.
Hope that helps,
Alex