I don’t know if there is a bug or no but that happened to me. In alliance war after I reached the 25000k skulls I should get a rune chest according to the reward box but I didn’t. The reward box marked the rune chest but I didn’t get that.
I think there is an actual display bug w/ runes chest.
They are displayed behind non-runes chest, most of the time they are behind daily quest chests
you were right, I found it behind my uber chests