Unfortunately this is not just an issue with Canon. Nikon QC is not so brilliant, in my experience anyway. Klaus on Photo Zone often refers to lenses having centering defects, whereby the lens elements are not correctly aligned in the lens cells. In the US I have heard it said that Canon will 'calibrate' a lens, which I take to mean realign the internal elements.

Anyway, I'm glad to hear that it was a happy ending to your story. I guess there is something to be said for Jessops then!