I've done some experimenting since updating to 1.1.6
If I tick the box to use Facebook comments on any of the 3 options (Posts/Pages/Attachments)a WORDPRESS comment box appears on my home page (this is set to a fixed page, not the 'latest posts').
I do not want comments on any of my fixed pages, and have stipulated this is the per-page settings by ensuring 'allow comments' is unticked on every fixed page.
If I do not tick the Pages tick box on the Facebook comments setting page, a WORDPRESS comment box appears on every fixed page.
If I tick the Pages tick box on the Facebook comments setting page, I get no comment box at all (which is the desired behaviour, based on my per-page settings).
I conclude there MUST be something in the plugin settings causing the WORDPRESS comments feature to appear where it shouldn't.
As it stands, I have no ticks in the Facebook Comments setting page, and WordPress comments are appearing as expected.