Yeah, the hounds were a bit tricky.
Also, another bug: apparently if you pray at the Shrine in the Shelter (where Gratiana is), and you get the holy water which heals you... well, the next time I came there, Gratiana was dead. She was dead apparently because healing damages her? And she got too close to the water?
Are you sure you didn't tamper with her soul jar in braccus' vault?