It's the light fall off from the lens as you go closer to the subject because the distance of the image plane to the lens will need to be further. So the apparent aperture is perceived to have decreased. It will not matter if you're using in camera metering but if you're using an external meter or non-TTL flash, you will have to compensate manually.Thats typical of all macro lenses...the aperture will stop down as you go down to macro level. Not sure how to explain it...happens to my friends 105VR as well as my Tokina 100mm Macro...
The only macro lens which doesn't exhibit this trait is the AF Zoom-Micro Nikkor ED 70-180mm f/4.5-5.6D