I have had this issue with the cipher not dropping in-game, but I got it on every character the first time I beat Skolas With it. My bounties were full twice, and when they were I didn't see it drop when I was still in the Prison; However, when I got to the Reef, and turned in bounties I went to postmaster and it was there. My son had the same issue, but it wasn't at the postmaster either. He didn't get it until he emptied the packages from the postmaster then went to Variks (I'm sure I misspelled that) and Cryptarch—It was there that he got it. Hope this helps.