Hi. From my experience with PMOD it seems that the displayed window of units is read differently. I would try several things if you want to spent some time on the issue.

1. Try to check the VALUE of the center of the white spot on that image on both versions of Mathematica. If the values are the same, so there is a rendering problem. If the values of the same point or area are different, maybe you read the values different way, for example WORD and REAL numbers.
2. PMOD and many other programs, when reading DICOM files they do not respect the predefined window of the units. It is especially important in CT images, where for example for brain scans you would like to look at -10...100 HU, while the image range in total is -1000...1000 HU. Maybe two different Mathematica versions treat the image in different way.
3. Check if the SAME version of Mathematica on different machines render the image the same way. Some DICOM reading programs tend to remember the unit window.

Hope that helps.

Marcin

Addendum:

The version of Mathematica does in fact make the difference:

Here we get an image with 125 different gray levels; using MMA v10 (in this case!) we get much less. Maybe somebody from WRI can comment on this.

Could you post the code that generated this image? That might be helpful. (Or a simplified example that behaves the same way, maybe something from the Documentation.) Is that on the same machine before and after upgrading, or on two different computers?