I'm running into this comment count problem, too, and having a tough time figuring it out.
Here's a
story that still says "Discuss" instead of "1 comment", but it definitely has a comment below.
The big clue to me is that the record for this story in the links table still has a link_comments=0. For some reason it wasn't updated when that comment was added, but I'm having trouble reproducing it.
The code is straightforward:
1) in libs/comment.php, there's a call to $link->adjust_comment(1); then $link->store();
2) in libs/link.php, the store() function calls store_basic(), which should update the comment count in the link table.
I'm about to break down and add massive logging and step through it. I'll report back if I find anything.