I found that the easiest solution was to turn off the flat tables and then get the SQL query that magento executes using the ->load(true) parameter
e.g.
$collection = Mage::getModel('catalog/category')->getCollection();
$collection
->setStoreId($store->getId())
->addAttributeToSelect('*')
->addAttributeToFilter(array(array('attribute'=>'ig_unifeed_ids', 'like'=>"%:".$this->getId().":%")))
->load(true);
then turn flat tables back on and replace this code with:
$resource = Mage::getSingleton('core/resource');
$readConnection = $resource->getConnection('core_read');
$query = "SELECT `e`.*, `at_ig_unifeed_ids`.`value` AS `ig_unifeed_ids` FROM `catalog_category_entity` AS `e` INNER JOIN `catalog_category_entity_varchar` AS `at_ig_unifeed_ids` ON (`at_ig_unifeed_ids`.`entity_id` = `e`.`entity_id`) AND (`at_ig_unifeed_ids`.`attribute_id` = '139') AND (`at_ig_unifeed_ids`.`store_id` = 0) WHERE (`e`.`entity_type_id` = '3') AND ((at_ig_unifeed_ids.value LIKE '%:".$this->getId().":%'))";
$collection = $readConnection->fetchAll($query);
From this point on you will probably need to change other code like replacing
$category->getId()
with
$category["entity_id"]
I hope this helps a bit...
NOTE: this is a real solution for the IG_Unifeed module magento bug that disregards category filtering when using flat tables.