The URLs aren't identical, one has "index.php" at the end, the other doesn't:

yada yada ... barak-obama-directs-all-federal-agencies-to-have-an-api/

yada yada ... barak-obama-directs-all-federal-agencies-to-have-an-api/index.php

With regards searches, it depends on what you search for. HN_Search is not always obvious, and it doesn't index minute by minute. You may have done the search before the engine caught up.