You are describing the same behavior that I get in my Honda.

The amount of time for it to be in "standby" after ignition-off is configurable. Please see the FAQ entry on this subject.

I also get the "thump" if I turn my ignition off then start the car again while it's still in standby. Reduce your timeout to a very short time period (say, a second or two) and this problem will go away I think.