So I've been trying to collect the Black Stones (for the story, obviously), and have reached the very end of the quest "A Song in the Silence" (the one with the weird kid and his wishes). I've finished the quest itself, and upon taking the stone from his corpse, the stone is not added to my inventory, which is obviously not the ideal situation when you need all 3 to continue through the story.
I have two mods in my game, one is a custom race (gourd), and the other is a custom weapons. The individual who converted/created these mods for me, has assured me that they shouldn't conflict with the inventory system, or quests.