Are you saying that when someone like's an article from your site.. if someone else clicks the "Like" in the wall post that is created, that it will count for the article on your site?
If so, unfortunately, that's not how it works. Because the like box can have a comment on the article, or other user entered information, the Like on the wall post is for the Facebook user's comment, not for your site. It still will post that comment to their wall, for their friends to see, with a link to your article, but doesn't add to the article's Like count.
Hope that helps explain. That is Facebook's design, and there's no way we can change that.