I seem to have a similar problem. I am thinking it might be mold in the grout. This is because I sealed the grout and the smell along with the dark color went away. However, a week later the smell returned. Also, the smell gets more intense after a hot shower is used. So I plan to have a mold remediation tech treat the grout with Hydrogen Peroxide this Friday. Although I am not sure if it would penetrate the grout sufficiently to kill all of the mold. But lets see if it works. Using vinegar may be another way.