The same sort of thing happened to me as well. After killing Scabban, I returned to the guild looking for the guildmaster to shower me with precious gifts as a reward. Didn't happen. After I finished the Crypt however, I returned to the magic shop once again and was given credit for completing the quest.
On a side note, I have not been able to claim my reward from the Mayor of Valeia for delivering his message to Ishad N'Ha's town hall. He keeps asking me if there's a problem. Um, yeah there's a problem...I'm not getting my reward. I decided to give up on that one.
Serath
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