What's the condition and charge level of your batteries?
I had a few batteries that wouldn't hold charges well back when I was using my 300D/30D/40D bodies and low battery level is one of the things that can slow down continuous shooting. I could see a weak old battery possibly showing enough charge after focusing in one shot but voltage dropping down enough to slow continuous shooting while Ai servo is running.
I know my 1DIV the drive mode icon will flash if battery level is low enough to slow drive speed, maybe the 40D will do the same(manual doesn't same anything about it and I'd test but my batteries for it are fully charged).




