One Drupal site affecting another cloned site
As beth, said in the comment, I am answering this, even after updating the question with answer.

The culprit was Memcached bin, since I am using memcahce_storage module for memcached, the bins of the main site and test site were same, hence, creating this confusion. 

I edited the settings.php page of test site and changed the prefix for memcached for test-site as $conf['memcache_storage_key_prefix'] = 'test_site';, now everything is perfect !!!