This happened to me. Everyone else said that my female Hero married Alistair but vanished. Morrigan however says otherwise. And I don't think the problem is with the Keep, it's with Inquisition. I'm playing the game in brazilian portuguese, a language that commonly differentiates genders for nouns. So Male Hero is called "Herói" and Female Hero is called "Heroína". While everyone calls her "Heroína", Morrigan calls "Herói". That's why i dont think the problem is with Keep.
PS: Calling her "Herói" is so odd that I thought she was talking about another Hero, not my Hero of Ferelden that stopped the Blight. Now I''m sure it's a bug.