I bought 2 Greater Seals of Malice from the store, and they didnt show up in my rune page, and the game still showed me as having 929 IP, yet when i went to rebuy them, it wouldnt let me, saying i had 109 IP.
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If you have a number of runes in your runebook, you might not be able to see new purchases. Try filtering by rune type to double check if they're there.
If they still don't show up, you can e-mail firstname.lastname@example.org and they should be able to complete your purchase.