I have just completed the Orc dungeon in the first act, and have brought the wife linda van gallahand back to town. I put here in jail, and was told she was set free because she was pregnant. I went to her house to advance the story, but she was not there. I found here still in the dungen, in one of the cells that cannot be opened. Is this a glitch that I can fix, if not, I need to start the entire game over again, as I have no save file before this.

Seems like a bug to me :( I didn't have any trouble there. Maybe others know more..

Edit: Or maybe you need to advance in the questline. After you complete everything, something will happen (I'm not saying what is for it would be a spoiler) and the game will go on.

Just do every quest in your questbook, and visit every places and talk to everyone. That will solve it, fortunately..

I have the quests for arresting the leader of the brotherhood, and have to investigate the death of the merchant, and also know that most of the bad things happening are all connected. Is it possible just to know if I should just look in the main village. Or is there something I missed? In my last play through, she appeared after being set free by the inquisitorial judge, and then she died after I spoke to her. What Is the next thing for me to do?

I was referring to her death while saying spoiler..

That should happen, yes, so you need to do something to trigger it. I don't know what, but it must be related to other quests. In the game, every single thing counts as advancement (and trigger). From talking to a beggar to burning a specific heretic..

Yeah sorry but it does look like a game-breaking bug. Like Excolion said, maybe try to finish every available quests and see if it puts her back in the village so you can talk to her like in your previous playthrough... If that doesn't work, well... you're pretty much screwed. The developers are supposedly working on a patch, so maybe you can wait for that (http://inquisitor-rpg.com/?page=forum ).