I had this same issue, WiccanWitch, as have most here, with this mod when I upgraded from 1.3.8a to 1.3.9h because this mod is flawed.

The fix was not perfect but simple and is explained in earlier posts. I don't know about the "seo urls" problem.

Here is the fix for Stock By Attributes - replace includes/modules/pages/shopping_cart/header_php.php with the one below from an earlier version of stock by attributes, namely stock_by_attributes_4-7MULTIADD. :

Code:
<?php
/**
 * shopping_cart header_php.php
 *
 * @package page
 * @copyright Copyright 2003-2007 Zen Cart Development Team
 * @copyright Portions Copyright 2003 osCommerce
 * @license http://www.zen-cart.com/license/2_0.txt GNU Public License V2.0
 * @version $Id: header_php.php 0000 2007-12-02 00:00:00Z kuroi $
 */

// This should be first line of the script:
$zco_notifier->notify('NOTIFY_HEADER_START_SHOPPING_CART');

require(DIR_WS_MODULES . zen_get_module_directory('require_languages.php'));
$breadcrumb->add(NAVBAR_TITLE);

// Validate Cart for checkout
$_SESSION['valid_to_checkout'] = true;
$_SESSION['cart_errors'] = '';
$_SESSION['cart']->get_products(true);

if (!$_SESSION['valid_to_checkout']) {
  $messageStack->add('shopping_cart', ERROR_CART_UPDATE . $_SESSION['cart_errors'] , 'caution');
}

// build shipping with Tare included
$shipping_weight = $_SESSION['cart']->show_weight();
/*
  $shipping_weight = 0;
  require(DIR_WS_CLASSES . 'order.php');
  $order = new order;
  require_once('includes/classes/http_client.php'); // shipping in basket
  $total_weight = $_SESSION['cart']->show_weight();
  $total_count = $_SESSION['cart']->count_contents();
  require(DIR_WS_CLASSES . 'shipping.php');
  $shipping_modules = new shipping;
  $quotes = $shipping_modules->quote();
*/
$totalsDisplay = '';
switch (true) {
  case (SHOW_TOTALS_IN_CART == '1'):
  $totalsDisplay = TEXT_TOTAL_ITEMS . $_SESSION['cart']->count_contents() . TEXT_TOTAL_WEIGHT . $shipping_weight . TEXT_PRODUCT_WEIGHT_UNIT . TEXT_TOTAL_AMOUNT . $currencies->format($_SESSION['cart']->show_total());
  break;
  case (SHOW_TOTALS_IN_CART == '2'):
  $totalsDisplay = TEXT_TOTAL_ITEMS . $_SESSION['cart']->count_contents() . ($shipping_weight > 0 ? TEXT_TOTAL_WEIGHT . $shipping_weight . TEXT_PRODUCT_WEIGHT_UNIT : '') . TEXT_TOTAL_AMOUNT . $currencies->format($_SESSION['cart']->show_total());
  break;
  case (SHOW_TOTALS_IN_CART == '3'):
  $totalsDisplay = TEXT_TOTAL_ITEMS . $_SESSION['cart']->count_contents() . TEXT_TOTAL_AMOUNT . $currencies->format($_SESSION['cart']->show_total());
  break;
}

// testing/debugging
//  require(DIR_WS_MODULES . 'debug_blocks/shopping_cart_contents.php');

$flagHasCartContents = ($_SESSION['cart']->count_contents() > 0);
$cartShowTotal = $currencies->format($_SESSION['cart']->show_total());

$flagAnyOutOfStock = false;
$products = $_SESSION['cart']->get_products();
for ($i=0, $n=sizeof($products); $i<$n; $i++) {
  if (($i/2) == floor($i/2)) {
    $rowClass="rowEven";
  } else {
    $rowClass="rowOdd";
  }
  switch (true) {
    case (SHOW_SHOPPING_CART_DELETE == 1):
    $buttonDelete = true;
    $checkBoxDelete = false;
    break;
    case (SHOW_SHOPPING_CART_DELETE == 2):
    $buttonDelete = false;
    $checkBoxDelete = true;
    break;
    default:
    $buttonDelete = true;
    $checkBoxDelete = true;
    break;
    $cur_row++;
  } // end switch
  $attributeHiddenField = "";
  $attrArray = false;
  $productsName = $products[$i]['name'];

  if (STOCK_CHECK == 'true') {
    $flagStockCheck = zen_check_stock($products[$i]['id'], $products[$i]['quantity']);
    if ($flagStockCheck == true) {
      $flagAnyOutOfStock = true;
    }
	  $stockAvailable = zen_get_products_stock($products[$i]['id']);
  }

  // Push all attributes information in an array
  if (isset($products[$i]['attributes']) && is_array($products[$i]['attributes'])) {
    if (PRODUCTS_OPTIONS_SORT_ORDER=='0') {
      $options_order_by= ' ORDER BY LPAD(popt.products_options_sort_order,11,"0")';
    } else {
      $options_order_by= ' ORDER BY popt.products_options_name';
    }
    foreach ($products[$i]['attributes'] as $option => $value) {
      $attributes = "SELECT popt.products_options_name, poval.products_options_values_name, pa.options_values_price, pa.price_prefix
                     FROM " . TABLE_PRODUCTS_OPTIONS . " popt, " . TABLE_PRODUCTS_OPTIONS_VALUES . " poval, " . TABLE_PRODUCTS_ATTRIBUTES . " pa
                     WHERE pa.products_id = :productsID
                     AND pa.options_id = :optionsID
                     AND pa.options_id = popt.products_options_id
                     AND pa.options_values_id = :optionsValuesID
                     AND pa.options_values_id = poval.products_options_values_id
                     AND popt.language_id = :languageID
                     AND poval.language_id = :languageID " . $options_order_by;

      $attributes = $db->bindVars($attributes, ':productsID', $products[$i]['id'], 'integer');
      $attributes = $db->bindVars($attributes, ':optionsID', $option, 'integer');
      $attributes = $db->bindVars($attributes, ':optionsValuesID', $value, 'integer');
      $attributes = $db->bindVars($attributes, ':languageID', $_SESSION['languages_id'], 'integer');
      $attributes_values = $db->Execute($attributes);
      //clr 030714 determine if attribute is a text attribute and assign to $attr_value temporarily
      if ($value == PRODUCTS_OPTIONS_VALUES_TEXT_ID) {
        $attributeHiddenField .= zen_draw_hidden_field('id[' . $products[$i]['id'] . '][' . TEXT_PREFIX . $option . ']',  $products[$i]['attributes_values'][$option]);
        $attr_value = $products[$i]['attributes_values'][$option];
      } else {
        $attributeHiddenField .= zen_draw_hidden_field('id[' . $products[$i]['id'] . '][' . $option . ']', $value);
        $attr_value = $attributes_values->fields['products_options_values_name'];
      }

      $attrArray[$option]['products_options_name'] = $attributes_values->fields['products_options_name'];
      $attrArray[$option]['options_values_id'] = $value;
      $attrArray[$option]['products_options_values_name'] = zen_output_string_protected($attr_value) ;
      $attrArray[$option]['options_values_price'] = $attributes_values->fields['options_values_price'];
      $attrArray[$option]['price_prefix'] = $attributes_values->fields['price_prefix'];
    }

		if ( STOCK_CHECK == 'true' ) {

			// Added to allow individual stock of different attributes
			unset($attributes);
			if(is_array($products[$i]['attributes'])){
				$attributes = $products[$i]['attributes'];
			} else {
				$attributes = '';
			}

			// End change

			$stock_check = zen_check_stock($products[$i]['id'], $products[$i]['quantity'],$attributes);
	
			if (zen_not_null($stock_check))
			{
				$flagAnyOutOfStock = true;
				$flagStockCheck = $stock_check;
			  $stockAvailable = zen_get_products_stock($products[$i]['id'], $attributes);		
			}
		}
  } //end foreach [attributes]
  $linkProductsImage = zen_href_link(zen_get_info_page($products[$i]['id']), 'products_id=' . $products[$i]['id']);
  $linkProductsName = zen_href_link(zen_get_info_page($products[$i]['id']), 'products_id=' . $products[$i]['id']);
  $productsImage = (IMAGE_SHOPPING_CART_STATUS == 1 ? zen_image(DIR_WS_IMAGES . $products[$i]['image'], $products[$i]['name'], IMAGE_SHOPPING_CART_WIDTH, IMAGE_SHOPPING_CART_HEIGHT) : '');
  $show_products_quantity_max = zen_get_products_quantity_order_max($products[$i]['id']);
  $showFixedQuantity = (($show_products_quantity_max == 1 or zen_get_products_qty_box_status($products[$i]['id']) == 0) ? true : false);
//  $showFixedQuantityAmount = $products[$i]['quantity'] . zen_draw_hidden_field('products_id[]', $products[$i]['id']) . zen_draw_hidden_field('cart_quantity[]', 1);
//  $showFixedQuantityAmount = $products[$i]['quantity'] . zen_draw_hidden_field('cart_quantity[]', 1);
  $showFixedQuantityAmount = $products[$i]['quantity'] . zen_draw_hidden_field('cart_quantity[]', $products[$i]['quantity']);
  $showMinUnits = zen_get_products_quantity_min_units_display($products[$i]['id']);
  $quantityField = zen_draw_input_field('cart_quantity[]', $products[$i]['quantity'], 'size="4"');
  $buttonUpdate = ((SHOW_SHOPPING_CART_UPDATE == 1 or SHOW_SHOPPING_CART_UPDATE == 3) ? zen_image_submit(ICON_IMAGE_UPDATE, ICON_UPDATE_ALT) : '') . zen_draw_hidden_field('products_id[]', $products[$i]['id']);
  $productsPrice = $currencies->display_price($products[$i]['final_price'], zen_get_tax_rate($products[$i]['tax_class_id']), $products[$i]['quantity']) . ($products[$i]['onetime_charges'] != 0 ? '<br />' . $currencies->display_price($products[$i]['onetime_charges'], zen_get_tax_rate($products[$i]['tax_class_id']), 1) : '');
  $productsPriceEach = $currencies->display_price($products[$i]['final_price'], zen_get_tax_rate($products[$i]['tax_class_id']), 1) . ($products[$i]['onetime_charges'] != 0 ? '<br />' . $currencies->display_price($products[$i]['onetime_charges'], zen_get_tax_rate($products[$i]['tax_class_id']), 1) : '');
  $productArray[$i] = array('attributeHiddenField'=>$attributeHiddenField,
                            'flagStockCheck'=>$flagStockCheck,
                            'flagShowFixedQuantity'=>$showFixedQuantity,
                            'linkProductsImage'=>$linkProductsImage,
                            'linkProductsName'=>$linkProductsName,
                            'stockAvailable'=>$stockAvailable,
                            'productsImage'=>$productsImage,
                            'productsName'=>$productsName,
                            'showFixedQuantity'=>$showFixedQuantity,
                            'showFixedQuantityAmount'=>$showFixedQuantityAmount,
                            'showMinUnits'=>$showMinUnits,
                            'quantityField'=>$quantityField,
                            'buttonUpdate'=>$buttonUpdate,
                            'productsPrice'=>$productsPrice,
                            'productsPriceEach'=>$productsPriceEach,
                            'rowClass'=>$rowClass,
                            'buttonDelete'=>$buttonDelete,
                            'checkBoxDelete'=>$checkBoxDelete,
                            'id'=>$products[$i]['id'],
                            'attributes'=>$attrArray);
} // end FOR loop


// This should be last line of the script:
$zco_notifier->notify('NOTIFY_HEADER_END_SHOPPING_CART');
?>
Quote Originally Posted by WiccanWitch420 View Post
Also, I just noticed that on the regular stock items that dont have attributes that it will let you add more than available to your cart and will not let you check out but it will not give you the normal message of
I found another problem. With regular products when you put them in the cart, you can put more in the cart than it tells you are available, It will not let you check out, but it will not give you the message of

Products marked with *** are out of stock or there are not enough in stock to fill your order.
Please change the quantity of products marked with (***). Thank you

These are for the products that dont have the attributes. =( '

So the customer could potentially put 2 items in their cart, when there are only 1 left and instead of the cart telling them that they Products marked with *** are out of stock or there are not enough in stock to fill your order.
Please change the quantity of products marked with (***). Thank you


It will not say anything.