mine is apparently a space issue. i'm sure they haven't appeared for a week for 1 of my villager, i wouldn't just forget that. i've solved it now though.
basically, i also covered my island but with paths so the rocks would stop spawning on certain areas. and it does need a clear 3x3 area (for the tree, unlike fossils) and one thing i noticed is that it needs to be on the 1st level. i don't know if this is accurate but i've never found a glowing spot uphill--pretty sure i have an open 3x3 there and that's basically where i expected some of them to appear, but they never do. like i said i'm not sure of it, it could be a flower covering the ground that can be an issue on my cliffs. now, i cleared an area near the beach and i saw one again yesterday & today.
and also, depending on how many characters you have, each of them would need separate 3x3 areas. it can't spawn on the same place for the reason that it has to be clear in order to plant a tree.