It's old, but I struggled over it multiple times. :-)
To solve this Problem I manipulated the _prepareEntityCollection of Mage_ImportExport_Model_Export_Entity_Abstract
in an own module Extension of Mage_ImportExport_Model_Export_Entity_Product
like this:
/**
* Rewrite of Mage_ImportExport_Model_Export_Entity_Abstract::_prepareEntityCollection
* for the purpose of getting the configurable products to the end of CSV file:
*
* Problem was:https://magento.stackexchange.com/questions/44368/magento-import-error
*
* Apply filter to collection and add not skipped attributes to select.
*
* @param Mage_Eav_Model_Entity_Collection_Abstract $rCollection
* @return Mage_Eav_Model_Entity_Collection_Abstract
*/
protected function _prepareEntityCollection(Mage_Eav_Model_Entity_Collection_Abstract $oCollection)
{
$rCollection= parent::_prepareEntityCollection($oCollection);
$rCollection->addAttributeToSort('type_id', Mage_Eav_Model_Entity_Collection_Abstract::SORT_ORDER_DESC);
return $rCollection;
}