I think... I found it.
The problem was not posts coming from usenet, it's on the local end when I replied to or started a new thread. What I did was add what I think is missing nntpdateline updates:
newthread.php
Code:
$DB_site->query("INSERT INTO post (postid,threadid, ..snipped.. ,iconid,visible,nntpdateline) VALUES (NULL,'$threadid',' ..snipped... ,'$iconid','1','".time()."')");
newreply.php.
Code:
$DB_site->query("INSERT INTO post (postid,threadid,title, ...snipped... ,iconid,visible,nntpdateline,inreplyto) VALUES (NULL,'$threadid','".addslashes(htmlspecialchars($title))."', ....snipped...,'$iconid','$visible','".time()."','$inreplyto')");
Unless I'm missing something I think that's it? At least it seems to work right so far. I'm still waiting on usenet propagation to see what they look like externally.