I think its due to misplaced parenthesis in the WHERE clause of the post_outgoing() function. As it is at the moment, it will:
either (get messages with no refs) OR (get aanything with a subject that doesn't start with Re: and is in this group)
Therefore it will match any message that has no refs. regardless of whether it's in the right group.
What it should be doing is:
(get messages with no refs or ones that have a subject that doesn't start with Re

AND (also make sure they are in the newsgroup that is currently being processed)
Here's the fix:
Replace line 750 which currently reads:
my $q2 = db_fetch("SELECT poster,newsgroup,subject,refs,body,threadid,postid FROM usenet_outgoing WHERE (refs <> ' ') OR subject NOT LIKE 'Re: %' AND newsgroup = ". $dbh->quote($$newsgroup->{'newsgroup'}));
With this line:
my $q2 = db_fetch("SELECT poster,newsgroup,subject,refs,body,threadid,postid FROM usenet_outgoing WHERE (refs <> ' ' OR subject NOT LIKE 'Re: %') AND newsgroup = ". $dbh->quote($$newsgroup->{'newsgroup'}));
Let me nkow if that fixes it. I can't actually test it at the moment coz I'm busy at work.