Wrong rune page used.
Usually happens on the first game of the day for a summoners rift map. It'll always show my first rune page as the option by default but in actuality the last rune page i used is active regardless of what it shows in the champion select screen. In my case, the first page is titled Kayle. If I don't physically click it and adjust it, it won't actually be the Kayle rune page. It'll be the last rune page I used the previous night. It'll show Kayle for the rune page during champ select but then once the champion flash cards appear and the game starts loading, I'll see I have the wrong key stone.
There is another indication of failure. During the champ select screen, if you click to adjust the rune page, It'll show a check mark on the first rune page and also on the rune page that is actually being used in the list.