You present a graph that is not only linear, but with values on the ordinates also much higher than my 255. I would ask you for as explicit an explanation as possible.
jpg have only 256 levels per channel (8 bit) but many DSLR including the Nikon D3000 take images using 12 bits (4096 levels) so you should be able to see 4096 levels in RAW images from your camera. I have not used the D3000 or AIP4WIN though so I have run out of ideas I am afraid.
Cheers
Robin