Okay, so today I found a bug with IntenseDebate that was causing user comments to not to sync/appear on the site. While it still is having issues (the people at IntenseDebate need to fix a couple of bugs with the service), it is now mostly working.
This bug affected several comments from as far back as nine months ago. I’ve gone through and fixed those comments so that they appear again.
Anyways, I fixed the bug and sent the patch to the IntenseDebate developers. Hopefully they can sort things out.