It would seem the quests are being completed properly, ie. the party loses the correct item on quest completion, and gains the appropriate rewards (xp, gold, etc.). So not a game breaker or anything. More of an unsettling expierence.
For example; unpon returning the Girdle of Piercing to the NPC in the Friendly Arm Inn, the quest log updates with the return of Hull's sword.
If there's a fix for this issue, or if anyone could point me in the direction of what you think could be causing the problem, that would be awesome, as I haven't been able to find much info through searching.