From what I've read Gerry, I doubt you'd get images as sharp as the 400mm F5.6. That lens is about as sharp as they come.
Have a look at :
Canon EF 100-400mm f/4.5-5.6 L IS USM Lens Review
Put in the 100-400 and the 400mm F5.6 You'll see the image is much sharper on the prime, which is what I'd expect.
That doesn't means you lens isn't wrong. Is it still under warranty? I'd be tempted to contact Canon to get them to check it for free. After all, it's supposed to be L glass. You pay one heck of a lot for that quality, you've a right to expect it perform.