You mention a lot of different software components. I’ll generally describe the behavior of the Facebook plugin for WordPress with comments without knowing the details of non-Core components.
The Facebook plugin for WordPress 1.3+ lists your existing WordPress comments before displaying the Comments Box. If Disqus writes comments to your WordPress comments database and your theme supports a comments template then the switchover should continue to list your existing WordPress comments.
The Facebook Comments Box stores comments on Facebook’s servers and encourages new comments on the page. The plugin retrieves comments from Facebook servers and wraps those comments in a <noscript> element for better search engine indexing and anyone else browsing your site without JavaScript.
The Facebook Comments Box displays comments in JavaScript in order of social importance to the current viewer (surface that comment from your Facebook friend before the person who commented “First!” right after the post went live). The Comments Box solicits new comments at the top of its display area.
If everything works as intended you should see:
- A list of approved comments associated with the post through the WordPress commenting system.
- A list of approved comments submitted via the Facebook Comments Box wrapped in a
<noscript> element and not visible to visitors with a JavaScript-enabled web browser.
- A Facebook Comments Box with a new comment authoring area up top and a list of approved Comments Box comments for the post below.
It’s possible something is outputting existing comments outside of your WordPress comments template. It’s possible existing Facebook comments wrapped in a <noscript> element are not wrapped in the expected <noscript> (you may have overridden this value with a filter).
