I do not know the answer but one should consider the fact that the effect of the same force varies significantly depending on how the force is applied. For example rocks are really robots if they are pushed but breaks apart more easily if you pull them from different sides.
In more engineering terminology, what I am trying to tell you is that atmospheric pressure, being uniform, should induce almost only normal stress, whereas your sister lying on your legs may induce significant shear stress. If human body is more robust under normal stress than under shear stress (I guess one needs to analyze stress-strain diagram for that), then it makes sense for you to feel pain in the second case.
This is just a guess though, I honestly do not know the answer.