I have an armature with the "adjust edit cage to modifier result" option selected on the modifier. The problem is the when I go into edit mode and select a face, I cannot get the pivot point to be the individual origin or median point.
That's how blender works, it could/should be reported as a bug.
The mesh is deformed to match the armature during edit mode but the manipulator widget doesn't get the same deformation. If you toggle the edit cage display on/off you should see that the widget stays in the undeformed location of the selected face.
The same thing is happening with snapping the cursor.
While the widget is drawn visually in the wrong location it still functions correctly, as do the keyboard shortcuts G,S,R.