Shadow Maps vs Stencil shadows
That particular spot on Training Mission is lit up when you have shadow maps turned on, but not when stencil shadows are on. Not sure why.
It's like there's an extra light source there that stencil shadows aren't taking into consideration. Not sure if it's supposed to act like the light coming from the window across the water, or ... ???
Level authors often use extra lights that don't seem to have a source to accentuate things or help make ambient light seem more dynamic. (EG: in Training Mission, along the brick corridor leading to the Builder warehouse for sneak training, there's a bright, white dual-line light towards the top of one building that acts like moonlight rays casting down).
Why stencil doesn't account for it, though.. not sure.