Amalgamated a Rune -- Rune Disappeared

I'm trying to figure out some things. I select "Amalgamate" in the horadric cube. I see in my inventory that some items go dark, some do no. I select a boss trophy I have five copies of. It amalgamates into a unique -- cool! I also see that runes are apparently selectable. I select a magic rune I have five copies of. I hold triangle to transmute and -- my 5 runes disappear. Nothing replaces them in the horadric cube grid.

Did I just lose them? Did they turn into material? Something else?