Rune Page BUG! PLS HELP

I just leveled up in LOL. So, naturally, I went to add in new runes and put points in my mastery pages. The only problem is this. I dont have all the runes I had before,on Marks, I don't have Magic Penetration or Attack Speed, on Seals, I don't have my flat health glyphs, and on Runes, I dont have my cooldown reduction. I though it just refunded them into the store. But look! Store Page If you look VERY Carefully, it says I own all 9 runes! When I go to my rune page though, this is what the runes look like! My Rune Page Again, If you look carefully, you'll find I only have 7 Cooldown Reduction Runes, and none in storage. Here is more proof to show what runes I am using Rune Page 2 (sry it looks weird)

PLS HELP!