The IMAP functions (also available if using Exchange) can let you do many things, like not only checking for the subject line, but the e-mail address too. All dependant on the system used for the helpdesk, and whether an incremantal mailbox number is used per query.
Also having as Sarah said, a unique number in the subject, which if missing, can either be forwarded to a human box, or the content of the message checked for the unique id, and dealt with accordingly.
It is not that much of a nightmare (just making a similar one myself)
$unseen=0;
$seen=0;
$insert=0;
$which=array();
$ip=gethostbyname("mymail");
$stream=imap_open("\{$ip/imap:143}INBOX", "user", "pass");
$msgs = imap_sort($stream, SORTARRIVAL, 0, SE_NOPREFETCH);
$MC=imap_check($stream);
$MN=$MC->Nmsgs;
for ($i=0;$i<$MN;$i++)
{
$msg = imap_header($stream, $msgs[$i],80,80);
if($msg->Unseen == 'U' || $msg->Recent == 'N') {
if ($msg->fetchsubject=="Insert data BRCCS")
{
array_push($which,$msgs[$i]);
$insert=$insert+1;
}
$unseen=$unseen+1;
}
else {
$seen=$seen+1;
}
}
This will simply check the subject line, but have a look at what can be looked at in the imap_header / imap_headerinfo and take it from there...