Hello. It may be a lens issue, rather than body... have you tried it with another lens? If you have, try cleaning the contacts and make sure it's not down to merely overlooking something, such as focus point selection.
If you've verified it's not down to settings or a lens issue, I would send it in to one of Canon's service centers. They're great to deal with and have an excellent reputation.
I've only dealt with their facility in Irvine, CA... give them a call beforehand to explain the issue.
Reviews of the service center:http://www.yelp.com/biz/canon-factory-service-center-irvine
Alternatively, if you're not on the West Coast you can find a facility closer to you:http://www.usa.canon.com/cusa/support/consumer/eos_slr_camera_systems/eos_digital_slr_cameras/eos_40d?pageKeyCode=25