Works for me now as well. Thanks!
I am only using the plugin to take posts from the blog and post them to an affiliated Facebook page. The comments that are vanishing are the ones posted by people on the blog site.
On my FB plugin settings, comments box settings, I have nothing checked in the “show on” setting.
I just updated the Facebook plugin to version 1.1.4 and the comments all disappeared on my main page. I then disabled the FB plugin and the comments reappeared. This is on a vanilla WordPress blog. Is there a way to install the previous version of the FB plugin until this bug is resolved?