When Boolean operator on an object interacts with children of the same object the update is delayed whenever location of the parent is changed. as well when the file is loaded the update is missing completely. it's probably the wrong update order. it needs to update children first then the modifier stack
System Information
Operating system and graphics card
Blender Version
Broken: (example: 2.69.7 4b206af, see splash screen)
Worked: (optional)
Short description of error
Exact steps for others to reproduce the error
Based on a (as simple as possible) attached .blend file with minimum amount of steps