I am not sure exactly what is wrong but after the patch this morning, quest ransack is not working properly.
For example, I ran The Lords of Dust this morning at Epic Normal difficulty. My previous run was on 9/27/16. At that time I was not under any Ransack penalties and I only ran it once. Yet, when I ran it just now, I was hit with a penalty as if I had already played it once today and I was also not offered any Commendations of Valor for a reward.
Next I ran A Legend Revisited, again on Epic Normal. My last run was yesterday, but after the previous quest I used /ransack to make sure it was off ransack, which it was. When I completed the quest I was hit with a penalty as if I had already run it once, today, and when I went to turn it in I was not offered Commendations of Valor.
Then I ran Old Tomb, New Tenants. My last run was on 9/25/16 prior to completing an Epic Past Life. Again, upon completing the quest I was hit with a penalty as if I had already run it today, and again, when turning it in, I was not offered Commendations.
If more people have the same issue it may be worth looking into.