Found the culprit. Weather All Natural has an option to use only the real lights.esp and change the name of the .bsa to reflect the file. I didn't see it as a suspect because it didn't have ManiSmityLitRay.nif in the .bsa. But turning off the All Natural - Real Lights.esp stopped the upper windows in the Missing Pauldron from being solid rectangles of light. The light shafts are gone completely, though.
Edit:
But since I know the culprit and it is not anything in my game, I can just enable it again and disable the light blocks in the Missing Pauldron. The windows won't be lit, but they will still be there without the blocks.