Having T4i AutoFocus Problems

I have read a thread in here where someone was having T4i autofocus problems. Everyone said they need to learn their equipment. If that is so, help me!

I walked around outside today with my brand new T4i (18-55 kit lens), my first DSLR. After I got home, I was a bit disappointed because it seemed like more than a few of photos were not in focus.

So I tried to test it.

I set up the T4i on a tripod and took a picture outside (aperture priority). I took a picture using manual focus and I focused on the central green tree branch. I then switched it to autofocus. The areas of the central green limb lit up with red lights to tell me that is what it was focusing on.

I downloaded the two pictures and created this split to show the difference. The top is the auto, the bottom is the manual focus. Please blow up to 100%.

I have the full photos on my gallery if anyone is curious. There is nowhere in the autofocused picture that is focused.

Is there something that I am doing wrong? Is it a bad lens? Help!

Thanks in advance.

Photo Information: F/6.3, ISO 800, 1/20 second