Have you tested the camera + lense combo using Lens Align-Pro or any similar AF microadjustment tools? I use a Canon 50D and 70-200mm IS MKI lense. After doing some testing and calibrating I discovered my camera lense combo had severe front focus issues +17 at the 200mm end. If you think you're getting different results than say a 200mm prime you've used then what you might have is a rear focus problem with your 50D and 70-200mm is mkII combo.