Target not keeping piston cylinder and rod in correct orientation in pose mode

I am doing a tutorial here: http://www.youtube.com/watch?v=UbU4ie7MTr8 While finishing the walk cycle, I noticed that the piston and piston rod were not aligned correctly. Unlike other bones, I can’t seem to fine tune the cylinder and piston rod bones in pose mode (maybe because they have target bones.) Can someone tell me why this happened and what I can do to fix it? I’m pretty sure the target bones were positioned correctly in edit mode.

http://i1130.photobucket.com/albums/m539/Blanco111/help39_zpsf24197d4.jpg

Blend file
http://www.pasteall.org/blend/24255