So then you should have a date and time in the snatched table hitrun row for that userid and torrentid yes?
PHP Code:
// Message users who have hit and run
$res = mysql_query("SELECT s.id, userid, torrentid, name FROM snatched AS s INNER JOIN torrents AS t ON s.torrentid = t.id WHERE hitrun <> '0000-00-00 00:00:00' && hitrunwarn = 'no'") or sqlerr();
The hnr message you recieved is called by WHERE hitrun <> '0000-00-00 00:00:00 which is if hitrun is not equal to 0000-00-00 00:00:00
So your hnr is working?