I have found that from time to time Facebook refuses to load additional comments, after much fruitless debugging i have had to conclude that this was/is a Facebook issue and out of my control.
I recently migrated to Disqus, which offers Facebook connect which from a users point of view is similar and allows them to comment after logging in via Facebook, Disqus allows allow you to connect through Twitter and a number of other services which is nice.
I understand this is not perhaps the answer you were hoping for however i can say based on my personal experience with Facebook Comments, Disqus ended up being our best solution.