Gosney,
v4.2.0 of JFBConnect is almost a year old now and not there have been multiple changes to JFBConnect to ensure compatibility with constant changes in Facebook's interface. The current release of JFBConnect is v4.3.4, released in early January.
With that said, I look at your page, and I'm not sure of any reason the comments would dissappear. I see comments on the page you linked too. I don't know which ones (or how many) are missing. The only thing I can see that may be an issue is that your page can be reached at both www. and non-www. Those are 2 different URLs in Facebook's eyes, and could have separate comments for each. However, when I go to the non-www version, I don't see any comments there either.
So, my suggestions would be:
* Go to the FB Comments Moderation Tool and check what comments show there and where they seem to be posted. Maybe that will give you some clues as to what's happening:
developers.facebook.com/tools/comments
* Upgrade to a newer version of JFBConnect which will definitely fix some issues and have new features. However, we've never heard of this problem before, so I can't guarantee it will resolve this problem.
Hope that helps get you started,
Alex