The combination should not really matter, considering it's all Canon gear. The body possesses the AF sensor and calculation side; the lens does the grunt work with its motor and other parts.
What is the "focusing issue"? Does it occur with specific subject matter? Or under specific lighting? Or is it just all over the place?
Vanbells asked a good question of whether this is the only lens that exhibits strange behavior. I imagine you have at least one other lens to try on this body. Do you have another body to try with this lens?
I searched a few forums and could not find anything similar to your problem. Lemons do happen, unfortunately. :shrug: