There's too little info, and Konami's announcement at TGS makes things a bit confusing. At TGS, it was announced that there will be three true runes in Suikoden 5.
The Sun Rune was known by then (and since then, confirmed that the Queen has had it attached onto herself for two years), and the Rune of Dusk was also revealed at TGS. The third rune was said to be "missing."
According to a fac who managed to play the demo for an hour and a half (possibly due to staff being lazy) stated that the other rune was the "Rune of Dusk," and that the Rune of Dawn and Rune of Dusk were subservient to the Sun Rune.
We'll need more clarification.