The perimeter light grey colored grout joint of my new shower stayed black for more than two weeks but lightened somewhat during the next week. When applying a sealer, it turned black again. The horizontal joint (in the wall) was applied over mastic on durabond. The other joints in the grey ceramic tile floor were applied over thin set mortar. My contractor speculates that the problem stems from a contamination in the tile itself or the mastic. He recommended that the ugly joint be covered with a white arcrylic latex tub and sink selant (which was done).
What is the actual cause of this problem and what is the recommended fix? Will the joint eventually get lighter if I waint long enough?

Grey grout should turn grey within few hours after application and should be ready to be sealed in just about 3 days.

What kind of grout did you use ? Premix or powder ?

Your contractor is taking the cheapest and shortest cut he can. It should be removed and redone not covered. I doubt the tiles was contaminated since it only runs along one edge. Who supplied the grout, him or you?

Btw: just noticed... you don't use Mastic over Duraboard. You use mastic over greenboard and Thin Set over Duraboard...