Now I understand. I'm not what you would exactly call a caulking expert but here's my 2 cents, others may chime in.
Silicone or some siliconeized (if's that's a word) caulk can be on the shiny side and contrast remarkably with your matte black tile and charcoal grout..
There are caulks out there that are not shiny. ColorFast is one of them and they have shades that will match up with any grout color put out by all of the major manufacturers. .ColorFast Caulk
There are probably many others as well. Some of the tile pros who have done work with matt black tile might have some other good suggestions. In the meantime, you need to get that caulk out of there. Time is not on your side. It's gets harder to remove with each passing day.
That's my opinion.