Do you have active d-lighting enabled? I have read where that will slow down the FPS.
The second part is probably the VR on the lens. My IS on my Canon lens can make whirring and clicking noises while it's trying to stabilize the image.
On a final note, "shutter speed" is completely different from what you are trying to explain. Shutter speed deals with the amount of time that the shutter would have to stay open and what you are asking about is "frames per second"(FPS).
I bought a new D5000 but i have a problem with its shutter speed it seems that its slow in comparison with 4fps ?
How can test, under which settings ?
A second problem when its too quiet i hear noises with i half press the shutter button its like a spring plus a machine moving .... is it normal to hear such sounds, i would expect the auto focus machine to produce such sound but is it loud enough ?

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic