I found out what was causing the runes and mastery pages to not change in champ select.

When you go to change your runes in champ select from 1 to 2, slightly move your mouse onto 2 and left click, even though it's selected and highlighted on, it doesn't switch over. This is why sometimes when you rush to change your runes and masteries at the last second you get screwed when you thought you did change them.