I found out the cause of my problems. It was the off center AF points had wrong information and hence threw the focus plane off alot of times.
Since the off center AF points are line type sensors, they are less sensitive. When you get the focus confirmation beep, it only means that the AF system thinks that it is in focus, but the off-center AF points have a larger error bar compared to the center cross sensor. Esp lens with aspherical elements/curvature may result in more error for off center points. Thankful for the Canon rep to sit down and look thru my pictures and find the root cause of the problem.
After the problem was fixed, off center AF points are accurate to f/2.8; when stopped wider, its adviced to work around the problem. Off-center AF at f/2.0 was 50-50 at times, while at f/1.4 it was not so good. They recommended to try using center point AF and AF-lock/recompose for f/2.0.