I have been wanting to can some rabbit. I'm glad to know you put the meat in there raw; I thought you had to cook it first, and then can it, and I figured that had to result in overcooked meat.
In fact, aren't you supposed to start with hot contents and jars? She's obviously been doing this for a while, and I guess she's never had a problem.
I think the meat looking raw at the end was just because it was night at that point, and you were seeing washed-out colors by artificial light. It's hard for me to imagine that it would still be raw after 45 minutes of steam under pressure.