If MArtin does not appear in the chapel there is no way to continue with the quest. Is this a bug? After I speak to the countess I then found Martin back at Cloud ruler temple and neither he nor Jaufre goes to the battlefield. I can't see a way round this.
Let me see if I get this straight: Martin, at Cloud Ruler Temple, tells you to go talk to the Countess. (At this point, in a properly working game, he should be wearing his Dragon armor and leave with Jauffre for the Bruma chapel.) You go to speak to the Countess--still at Castle Bruma--and she should agree to meet Martin. At this point she leaves for the chapel, and you should follow.
Upon the Countess reaching the chapel, Martin should already be inside, and he and the Countess will start to talk. Are you saying that Martin never leaves Cloud Ruler Temple at all, so the Countess walks into an otherwise empty chapel?
What's your last journal entry for this quest?