As for the Rune of Beginning, that in and of itself is a True Rune. It's been argued that the Bright Shield and Dark Sword are not true runes, only portions that make up a greater rune. That being said, I still speculate that Jowy and Riou therefore possess the Rune of Beginning, but its shared between them. The rune activated after their duel and True Runes just don't turn on and off like that. They have to be put to rest or "break the seal" as mentioned in SIII, which happened after their duel.
Anyway, as for Windy, I think its safe to assume her method of possessing two true runes is something not even Hikusaak knows, after all, if he did then he wouldn't have to keep making clones. Then again, he may have two true runes, we just don't know. Regardless, I'd still love to see Windy reappear sometime. I thought it was total crap she didn't come back in SIV, but then, I thought the whole game was executed poorly.
"It doesn't matter if the glass is half empty or half full...what matters is the glass."