Magento – Catalog URL Rewrites index stuck

As mentioned in the comments you might be using two different php.ini files.
To check that please change the throw new Zend_Db_Adapter_Exception line to

throw new Zend_Db_Adapter_Exception(
  'pdo_mysql extension is not installed. php.ini:'
  . get_cfg_var('cfg_file_path')
);

and compare the result with the output of

var_dump(get_cfg_var('cfg_file_path'), extension_loaded('pdo_mysql'));

in your command line script.

see also:
http://docs.php.net/manual/en/function.get-cfg-var.php
http://docs.php.net/manual/en/function.php-ini-loaded-file.php
http://docs.php.net/manual/en/function.php-ini-scanned-files.php

It means there was a Magento or PHP error after the payment API request was sent, but before the order could be created in your Magento system. There's three places in Magento's codebase where that wording is used for an exception.

app/code/core/Mage/Authorizenet/controllers/Directpost/PaymentController.php
94:            $result['error_msg'] = $this->__('There was an error processing your order. Please contact us or try again later.');

catch (Exception $e) {
    Mage::logException($e);
    $result['success'] = 0;
    $result['error_msg'] = $this->__('There was an error processing your order. Please contact us or try again later.');
}

app/code/core/Mage/Checkout/controllers/OnepageController.php
553:            $result['error_messages'] = $this->__('There was an error processing your order. Please contact us or try again later.');

} catch (Exception $e) {
    Mage::logException($e);
    Mage::helper('checkout')->sendPaymentFailedEmail($this->getOnepage()->getQuote(), $e->getMessage());
    $result['success']  = false;
    $result['error']    = true;
    $result['error_messages'] = $this->__('There was an error processing your order. Please contact us or try again later.');
}    

app/code/core/Mage/Paypal/Model/Api/Nvp.php
987:            Mage::throwException(Mage::helper('paypal')->__('There was an error processing your order. Please contact us or try again later.'));

if (!$this->_validateResponse($methodName, $response)) {
    Mage::logException(new Exception(
        Mage::helper('paypal')->__("PayPal response hasn't required fields.")
    ));
    Mage::throwException(Mage::helper('paypal')->__('There was an error processing your order. Please contact us or try again later.'));
}

As you can see, in each case Magento will log the exception before re-throwing it. This means an error will be logged to your var/log/exception.log (assuming you have logging on). If turning on logging is too much for you, you could add temporary debugging code. Something like

var_dump($e->getMessage());
exit;

in the exception blocks. (Since this isn't PayPal related, I'm guessing that third use of the error message isn't the one you're seeing).

When Magento code catches a non-Magento exception, it typically uses a generic error message to hide (possibly sensitive) PHP system information from end users.