Bug with store cookie handling in Magento up to 1.6 if specifying a non-default store MAGE_RUN_CODE

gistfile1.diff

--- a/app/code/core/Mage/Core/Model/App.php
+++ b/app/code/core/Mage/Core/Model/App.php
@@ -511,11 +511,7 @@ class Mage_Core_Model_App
 
         if ($this->_currentStore == $store) {
             $store = $this->getStore($store);
-            if ($store->getWebsite()->getDefaultStore()->getId() == $store->getId()) {
-                $this->getCookie()->delete(Mage_Core_Model_Store::COOKIE_NAME);
-            } else {
-                $this->getCookie()->set(Mage_Core_Model_Store::COOKIE_NAME, $this->_currentStore, true);
-            }
+            $this->getCookie()->set(Mage_Core_Model_Store::COOKIE_NAME, $this->_currentStore, true);
         }
         return $this;
     }

Has this been fixed in 1.6+?

I'm having a massive headache trying to manually override the store cookie. It never seems to pull from anything but the cookie that is set (which causes issues by not reading the cookie until the second reload)

Even implementing the above diff doesn't seem to help in my situation:

http://stackoverflow.com/questions/18068999/magento-and-wordpress-synchronizing-menu-across-both-platforms-issue-with-coo