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;
     }