ive isolated addons and looks like handynotes is doing this.
the handynote plugins i run are mysterious camel figurines, wrath of the lich king, netherwing eggs, and map notes cataclysm. disabling each one of these plugins doesnt do anything, and there are no handynotes options to even try changing anything.
one thing i did notice was that changing the map size on elvui would temporarily change where the squares were, or remove them, or do nothing at all. however even with elvui disabled it still happens so its not that.
screenshot:
https://ibb.co/215NsPvZ
Could try /fstack to get the specific name of the boxes and that might lead you to the setting in HandyNotes or whatever addon.
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