Ok! So, the 6th file is in same floor as the chappel. In the bathroom look under one of the toilet doors you should see it.
The 11th file is a secret file as in the main game with the cheese note. And unfortunately it's at the very end of the Penumbra map... so it's quite a long way to reach it. (Not really worth it anyway it's just a picture)
I tested the puzzle in the bunker and it does work. But i noticed it's quite easy to press too many times on the valve without noticing it... I did it the first time, but when i restarted and redo, it worked. Maybe you pressed one of them too much times? It really is 3,1,2,2,2,1,3 .. In the order you access the valves it means first, second, third, third, third, second, first. Each one of them open a wall for that secret area, there's 3 tiny walls blocking the path basically. Turning one of the valve more than needed just re-close the wall.