@The Silent Shadow - one thing you could try. Go to an interior cell like an Inn. Wait 40 in-game days. This should reset most cells in the game. It isn't a guarantee, but it might fix this for you to finish the acheezement! Good luck!
Meridia's Beacon is a random loot item. First time I found it, it was in a chest in Valtheim Tower. The Beacon has no set spawn location.
I didn't know you could activate the quest without having looted the Beacon.
You can. If you go to Meridia's Shrine first (which is what the OP did), and activate the shrine, you're given the quest to get the Beacon from a specified "radiant" location.
I did the same thing, I got Meridia's Beacon in a chest in a Nordic ruin IIRC.
Meridia's quest will also start as soon you got Meridia's Beacon in random loot.
Yes, but the quest can also be started without the Beacon, by activating Meridia's Shrine. In this case, it's no longer random loot; it becomes a radiant quest item, in a specific location. That's what the OP did.