I had the same 'thump' just before a sound played, but only when my MacBook was running on battery, and only after a period of inactivity. Now after 10.4.10 the 'thump' occurs even when my Mac is plugged into the power. It's really irritating!
Seems that the audio system goes to sleep after a period of time, and can be woken up by any sound event. Makes sense to shut down the sound subsystem to save battery power, but it's useless when you're plugged in to an outlet.
Fix it please Apple! 😡