Most likely, this is due to unequal current density on the parts. I would expect that the darker parts are closer to the cathodes? I suspect that the portion of the part that is closest to the cathode is getting more current, which is building up a thicker anodize film (oxide layer).
Are you dying the parts after anodizing them? Dying the oxide film can be tricky, but usually you can increase the time in the anodize bath to help smooth out any inconsistencies.
If you are not dying the parts, I would greatly suggest that you try to make the part equal-distant from the cathodes or use auxiliary cathodes.
More info might help us. What type of anodizing is this? Type I, II, or III? What is your process? Seal type?
-Dustin Gebhardt,
CEF
Plating Engineer
Danaher Tool Group
Gastonia, NC