were you able to open the Bishops cupboard, to satisfy the (find info objective?) If so the same key opens the desk. The passageway leads to or from the storage room under the kitchen. There is a button to open the door in the floor in the kitchen, also can be opened from the ladder, under the kitchen in the store room. The two doors that are locked can only be open from the key on the other side. There is a secret button at the end of the long hall that has the hay in it on the other side of the torture chamber. it is on the left wall when facing the hole in the wall with the spider web. It has a glyph on it. It is hard to see but does highlight. You don't even have to get in there to finish the mission, if you don't want to. You might have to fight in there. LOL I hope that helps. As for the bugs, TDM can be buggy for some reason? Some times I restart and the same things don't happen again? Go figure.
Thanks for playing, and I hope you had fun!