I replaced your code with this loop cobbled from the example in Mail::POP3Client:

use Mail::POP3Client;
$pop = new Mail::POP3Client( USER     => $username,
                             PASSWORD => $password,
                             HOST     => "localhost" );
for( $i = 1; $i <= $pop->Count(); $i++ ) {
  open(MESSAGE, ">message$i") or die "Can't open message file";
  print MESSAGE, $pop->Body;
  close MESSAGE;
}
$pop->Close();
[download]

I haven't tested it, but I bet you can get this working sooner than your version.

..Theo