Parth, the problem you describe has happened to a few others too, including me. I still have no clue why once in a while Shinwiki will not accept that you've completed the quest. I'm pretty sure I did everything right, because it happened to me on my 4th time through, and had no problems the first 3 times. One thing I did differently: I went there before finishing the crypt, or even entering the Asylum. But someone else told me he did that too and did not have a problem.
So I have no solution for you, only consolation that it probably wasn't your fault, and that you don't need it for the rest of the adventure.