Solved it. When you init a new FTD, I needed to

sub init_FTD
{
    my $FT = Win32::FTDI::FTD2XX->new();
     unless( $FT->PFT_STATUS() == FT_OK )
  {
    printf( STDERR "FTD2XX::new() failed: %s (%s)\n", $FT->PFT_STATUS_
+MSG(), $FT->PFT_ERROR() );
    return 0;
  } 
  printf( "FTD2XX::new() allocated PFT_HANDLE: %d\n", $FT->PFT_HANDLE(
+) );

#    $FT->PFT_DEBUG(1);
    unless ($FT->OpenByIndex(0))
    {
        print "Problem opening Port 0\n";
        return 0;
    }
    unless ($FT->SetBreakOn)
    {
        print "failed to set brake\n";
    }
    unless ($FT->Purge(FT_PURGE_RX))
    {
        print 'cannot purge';
    }

    unless ($FT->SetBaudRate(FT_BAUD_2400))
    {
        print "Baud is set\n";
        return 0;
    }
    return $FT;
}
[download]

otherwise all the data that comes in is seemingly junk.

That was incredibly painful to figure out. I knew I would get there though, once I asked for other people's assistance. Its the way of things.