Tony, how many active focus points do you have in play? It sounds like you might be letting the camera choose the AF point instead of you making that decision. The camera has certain rules it follows for making these decisions, but they may differ from what you are expecting it to do. Try using a single AF point, or even spot AF. That should let you snipe your target instead of having the camera pick some alternative subject through no fault of its own. The more complex the environment, and shooting birds in trees can prove demanding, the more important it is to narrow down the focusing scope, so the fewer points in use the better for such situations. For birds against clear skies that's another story, but for birds in trees, with possible backlighting from the sky, you need to set the camera up for success, not failure.
Also be aware that the behaviour changes depending on which AF pattern you choose and whether you are in One Shot or AI Servo mode. If you're using AI Focus then that could be a source of major problems. It's a pity Canon ever included it on any of their cameras. The professional bodies don't have that option at all.
I've got a whole bunch of birds in bushes examples from my 7D in this thread -
http://www.talkphotography.co.uk/forums/showthread.php?t=409438&page=2. They're not necessarily pretty, because they were shot purely as examples to challenge the AF performance. The camera can certainly deliver the required results, but it has to be set up right and used correctly. With so many options available the scope for setting it up poorly is potentially significant.
