Did you try simply burst or single shot firing and paying close attention when performing melee/jump actions? Try those on the 40GB model to see if you see any delay. Also, was the controller plugged in via charger? And what was your TV?
Home I have a couple year-old LCD (HDMI), I was using my DS3 controller wirelessly.
Work is a monster projection TV (Component), was using DS3 controller connected via USB. I don't notice any difference. I'm pretty used to the game though -- seemed mildly laggy at the beginning, but I just don't percieve it anymore. Only took about 30 mins of playing before I no longer notic ed. Frankly, I love the heavy feel, which is why I'm not gonna gripe about it. Superspeed and hopping around levels is lame, and always has been.