Well, shooting in shutter priority 1/1250 @ ISO100 with 100-400 L IS
probably caused the aperture to open up to 5.6, and if you were shooting anywhere near 400mm, that's a pretty bad combination. This lens often doesn't perform too well at both extremities (long focal length and open aperture).
I'd recommend using Av around 8.0 with ISO100. You could even bump it up to 200 with the 40D; it performs pretty well with higher ISOs. Looking back at airshows this summer, this combination was still giving me a decent 1/640 (~1/1000 with ISO200). Other than a few autofocus problems, I was getting tack-sharp shots with the 40D+100-400 combo shooting F-15s and F-22s in Oshkosh.