if your pop mail box is overloaded, here's a script to bulk delete messages. fyi, messages are stored from oldest to newest.
$server = "mail.domain.com";
$username = "username";
$password = "password";
$max_delete = 100;
set_time_limit(300);
$pop3 = imap_open('{'.$server.':110/pop3}INBOX', $username, $password) or die("error");
$num = imap_num_msg($pop3);
for($i = 1; $i <= $num && $i <= $max_delete; $i++)
imap_delete($pop3, $i);
imap_expunge($pop3);
imap_close($pop3);