Incorrect runs/masteries after pick/ban?

This has been an inconsistent problem for me for a while, and I thought I had figured out a fix (switching between runes and masteries at least once before pick/ban phase is over) but for some reason now, no matter what, it only selects my top rune page. Before I had sometimes had problems with my masteries being wrong as well if I didn't double-check them by clicking them twice.