In the blend file you'll find two bones that in edit mode are perfectly overlapped but in pose mode they have an offset, even if the rig is in Rest Position.
The only reason I find for this to happen is the use of the "Apply Pose as Rest Pose" operator. If you run that operator multiple times you'll notice that the offset between the two bones gets even worse.
Even though the Apply Pose operator could be the cause of this undesirable offset, I've found out that this started to happen only after blender 2.71. If you open the file with Blender 2.70a, you'll see that if you toggle between Pose mode and Edit mode, the offset is fixed!!