Code:
      if (zen_get_shipping_enabled($this->code)) {
        $this->enabled = ((MODULE_SHIPPING_FREESHIPPER_STATUS == 'True') ? true : false);
      }


// bof: turn off for manufacturers_id 3
if (!IS_ADMIN_FLAG) {
  $chk_man = $_SESSION['cart']->in_cart_check('manufacturers_id','3');
  if ($chk_man > 0) {
    $this->enabled = false;
  }
}
// eof: turn off for manufacturers_id 3
If using UPS you need to customize the file:
/includes/modules/shipping/ups.php

in a similar manner:
Code:
    // disable only when entire cart is free shipping
    if (zen_get_shipping_enabled($this->code)) {
      $this->enabled = ((MODULE_SHIPPING_UPS_STATUS == 'True') ? true : false);
    }

// bof: turn off for manufacturers_id 3
if (!IS_ADMIN_FLAG) {
  $chk_man = $_SESSION['cart']->in_cart_check('manufacturers_id','3');
  if ($chk_man > 0) {
    $this->enabled = false;
  }
}
// eof: turn off for manufacturers_id 3