What portions of the brain have drastic changes in activation when we "sense" someone is there?
First of all one should tell that one can attribute the activation of certain brain zones with some indepent events only when the activation takes place along the signal input (receptors, sensory pathways towards the cortex and the sensory areas in cortex) or motor action (=output) (along the motox cortex => motor neuron => target organ). Those zones in brain are also termed as primary ones, for there is a clear mapping between the event/action and the activity here.

In case of your "sneak feeling" as you describe in your post, there seems to be more not the sensory input from some unknown type of receptor, but rather a subconscious processing of the complete sensory input that reveals some potential danger and is percepted as a kind of "smell of danger". Since this processing happens in secondary zones and can be well distributed throughout the whole brain, there is no possibility to find a single focus with high activity change here (in my opinion, of course) -- those changes in activity are beyond the measuring/imaging capabilities of modern examination methods.

Possible sensory inputs here might include (but not limited to):


Optical (some shades, moving asyncronously etc).
Acustic (some sneaking sounds, normally disguised by the background sound).
Air move, air stream blocking sense etc (tactile feeling).


So, everything you suggest might apply here.