My loader scripts call ensureIndex to allow the database to automatically be generated, however it turns out that the current release of the perl API doesn't support the expiresAfterSecond argument, which I discovered after creating the index. Therefore I remove the index and created one in the background from the mongo console. Meanwhile my script restarted, which resulted in the database becoming corrupted (luckily recover did succeed). Have distilled out the underlying issue in an attached script.