My TV is set up so that most games look fine at their default brightness setting. Dishonored was fine to begin with - on the calibration screen I could just see the far left symbol and the graphics looked good. However, upon reaching the Hound Pit Pub and going on the first mission the game looked washed out and the low res textures became really noticeable. I had to lower the brightness setting about 10 notches below the "correct" setting to get the graphics looking good again, with properly dark shadows. On the calibration screen half of the symbols were too dark to see but the in-game graphics were fine. I went back to the prologue and prison level and the graphics were now too dark at this new brightness setting.

It's clear that the in-game brightness changes after the sewer and is set too high. So if you're finding the graphics less than impressive try setting them again after the sewer and use your own judgement, not the in-game calibration.

Edit: But now with the lower brightness setting Dark Vision is too dark! I can see people through walls okay, but I can't see my surroundings very well, even though it says in the description that Dark Vision should let you see in the dark. Oh well, that should stop it being over powered...

Wonder if the global light setting was set too high, or low in one place. One thing, some TV's have a dynamic adjustment to lighting that tends to overcompensate. Was the room lighting different in these sections, like one was in the afternoon and one in the evening? Try turning off the dynamic adjustment on the TV and see if that evens things out.

Are you sure it's not just the game's brghtness adjustment based on your play?

I know, same thing for me. I think I like it better that way though, because - as you mentioned - it actually balances the power quite nicely. And after all, it IS called Dark Vision...

Overall I didn't notice a severe change in brightness between missions, although I changed my brightness level after the 2nd mission...