Thanks for your input.

I must not have expressed myself as clearly as I thought... (wouldn't be the first time, probably won't be the last;) I'll try again, in case someone with enough authority and time sees this and decides to look into it.

The problem is not that I was surprised to see only direct replies, it's that I saw too many replies - almost twice as many as I expected in some cases.

To duplicate the issue, go to User Settings and check "Show count of all replies". With this setting on, I see "9 replies" next to need to extract top and bottom lines... on the front page, but there are only 5 replies total (including replies to replies) when I check the actual node.

With that setting turned off, I see 5 replies.