Tim, were these shots taken withthe 100-40L or the 400/5.6L?
All with the 100-400. I don't have, and have never owned or used the prime. But I don't doubt those who say it is sharper wide open and faster to AF.
Here's an example from the album at 285mm (you can't do that with the prime

), but with a shutter speed of 1/1600, and the bird moving swiftly in a diagonal direction, IS would have been of no use at all. In fact, in my experience it would quite possibly have been detrimental.
The idea behind Mode 1 IS is to stabilise the lens and counteract the effects of movement at the camera/lens end of things. If your intent is to move the camera, which you usually do for BIF, then the IS will fight your movements and result in a jerky image in the viewfinder and potentially odd effects in the captured image. Mode 2 IS is designed to freeze motion EITHER horizontally OR vertically, while you attempt to pan smoothly in the other direction. If your subject is moving diagonally then mode 2 IS won't help either.
Mode 1 IS can be advantageous if you have a bird coming straight at you, where you have no need to pan, or where a bird is travelling in level flight across your field of view, requiring no panning in a vertical direction. However, any movements such as landing, swooping etc. are just not going to work well with IS engaged, at least in my experience. Take a look at this example....
One moment I was tracking the bird horizontally (more or less) and then suddenly it soared upwards to catch some food. I have no clue what IS would have made of that little manoeuvre, but in the past I have had results which you would think would be perfect, yet ruined because the IS didn't have a clue what to do and crapped all over the image. Needless to say, I have learned from those experiences and now leave IS disabled for such shooting.
There is also an interesting article by Thom Hogan in relation to Nikon's VR system, where he cautions against the use of VR when using high shutter speeds, and he explains why. I would not be surprised if similar concerns apply to Canon's IS system and other similar systems. Here's the article....
http://www.bythom.com/nikon-vr.htm