Originally Posted by Tabazan
Yes, it does seem strange. HDNitehawk had some good suggestions, to help identify the problem.
Tripod to eliminate camera motion, stationary subject to eliminate subject motion, and try2 different lenses if you have them. Also try to get squared to same plane as your subject, as opposed to shooting on an angle.
Please forgive me if I am over simplifying this, since I don't know your level of experience with Canon, but if you are in One shot mode, then make sure that the red square is lined up on your target and then press the shutter button half-way to achieve focus lock. You should then hear the beep and then press the shutter button the rest of the way to take the photo.
Just remember, it is more important where focus lock was initiated, and not where the red square ends up, as occurs in re-composition.