When you enter the cavern with the small pool and several rats (two spiders before the patch) there are two passages to exit from. Each will appear to end with a "dead end" but if you use the empty torch holder located nearby a section of wall will drop.

Secret #3:

   In Sheriff Truart's office, one of the metal figures opens a passage behind the fireplace. In the connecting room a switch near the wall opens the other part of the passage leading to the second floor of the Training Room. If you're coming up from the Training Room use the empty torch holder in the small storage area at the rear of the Training Room. Before the patch opening both parts of the passage were considered secrets, now its just one.

Thanks to Matt & Sean for the info.

Secret #4:

   In the Warden Affairs office on the second floor, turn left and jump atop the desk. One of the books in the shelf can be moved to open a passage. This connects to a room located on the south eastern corner of your map of the third floor. If heading the other way, go to the most south eastern room of the third floor, head to the south east corner and find the book that sticks out. Before the patch, opening both parts of the passage were considered secrets, now its just one.

Secret #5:

   In the Target Range, shoot an arrow into the furthermost bullseye, it will cause part of the wall to open giving you access to the armory. (and worth it!)

Secret #6:

   A passage can be opened connecting the Main Office to the adjacent hallway near the barracks. When entering the Main Office head to the back right corner and look for the switch on the wooden support. In the adjacent hallway the "switch" is an empty torch holder.

Secret #7 & #8:

   Use a rope arrow to mantle the trim of the Main Office's northern wall. A switch nearby opens one of the vents. The passage beyond connects to the Secured Records area. Going the other way, head to the southern end of the Secured Records room and pull the book that sticks out.

Secret #9:

   This new secret was introduced with the patch, or rather counted as one since this hidden compartment was present even before the patch. In the Front Office where the alarm control panel is located. Look with care under the alarm panel for a button that opens a small section of the floor under your feet.

Thanks to everyone who pointed this out, didn't think the patch was gonna change secrets around.

Easter Egg:

   At the beginning of the mission, toss a scouting eye over the spiked wall on your left. Look around and you should see something a bit...err....out of place.