I have 3 sites that I worked on last night (3/3/12), matched them all up to have the same settings (but different FB app id & key). I had them all working great. A few hours later, I noticed there weren't any comments. I've tried for hours today to find the problem... no luck. I've tried different browsers, different themes, even different plugins. No luck. I can see the comments in moderation at FB/developers.
Could it have something to do with WP v3.3.1? I could have sworn I did a new install with 3.3.1 and it worked.. initially.