OK, it happens on all lenses, so it's your AF rather than IS, and it happens to some degree with the 40D, so it must to some degree be "normal". It is likely related to your AI Servo AF trying to focu on the moving object -- you say birds in flight -- are these birds close enough to fill the center of the viewfinder?
Maybe you could test things out on some things that are bigger, such as cars driving down the road. If the AF is jumping around when you are focusing on a fairly large object, that would be a problem, but you want to compare with the 40D to see if it's out of whack with the 50D.
With small objects, AI Servo will try, but sometimes fail, to focus on the object, and may hunt back and forth and around the center. The actual "point" of focus is larger than the little dot that flashes on the screen, and so you may see the camera focusing on something a bit off-center.
Birds in flight are tricky things and take practice. That's why I suggest testing and learning using larger objects, such as cars, airplanes, bicycles, boats, etc.