Grimoire Mastery

After investigating, as far as I can tell, this works fine. The weapon is creating an entry in the relevant list, and comparing an account before/after using the Grimoire,  there is a difference of 3000 mastery for the Secondary Weapons category in the profile.  Verifying with some player accounts from this thread, the quest does increase the weapon's level automatically, but the mastery progress is credited to your account when you finish the mission.  Possible reason for your confusion: by the time you checked your profile to see if you had got progress or not, it was too late to get a "before" value because your mastery went up the 3000 points it should have in the middle of the quest.