Update: I did another small test area without misting the substrate. The grout dried seriously darker than what was left in the bucket or what it is in the surrounding tile.

I also called Custom Building Products, the grout manufacturer and a technical support person reviewed my photos and guesses that there is something in the subsurface (thinset of mudpack under the floor tile), such as old soap scum or body oil, that could be leaching into the grout. However, he is not sure. He also said that grout stains are available, but they are not good for shower floors.
Anyone have any ideas or experience with this type of problem?

I find that it is usually just a difference in color in the grout lot. Pro tilers mix all of the dry grout together before an installation to make sure the color is homogenous.
I have the same problem in my bathroom. Same manufacturer, same color on the label, different color on the floor. I don't have any idea how to match it.

That was my first thought. However, the leftover grout in the mixing bucket is almost identical to the original color in the rest of the shower. But the same grout in the joint dried substantially darker. Real mystery.