When shooting in automatic, make sure you press the button half way down to focus before you take the photo. If it is not focusing on the main subject, then you are too close to the subject.
What kind of macro lens are you using? If you're using a 50mm to 60mm lens, you still have to be a good 3 to 4 inches away from the subject in order for the camera to focus.
You can also set your dial to the little flower (macro setting) to see if that helps.