I have retrieved the Skull, the Milky Rock, and the Glowy Vial. I have placed the Skull on the Lord's Altar, but I can't place either of the other items on any altar. The menu option upon examining the altar just isn't there. The Pale Sentinel is telling me I have everything.
If it helps, earlier I tried to place one of the items on the 'wrong' altar and got a bit of red local lightning.
I have left the location and re-entered. I have left the game for days, hoping for some kind of reset.