Using colors on the Fortus systems is a great way to make your parts stand out, especially when creating an assembly or specialty parts for manufacturing applications. (Designated colors could signify safety, caution, no-fly, danger, etc.)
However, one thing I've noticed is that after using a colored material, when I switch back to a lighter color or natural material, some of the darker colorant bleeds onto the first few layers of my next part. I could purge extra material during the loading process, but that wouldn’t create any back pressure in the liquefier; some colorant will remain in the tip until building an actual part.
To prevent this, I created a small coin-like part the size of a quarter using Insight. I generate toolpaths without generating supports and build this color-purge part before my actual job. It only uses about 0.2 cubic inches of material and takes about 10 minutes to build. This ensures that the colorant is completely removed from the tip before starting my job. Give it a try on your next color change.