Dear Lucky:
Obviously your slate is extremely porous.
Jason's concern is right on the money. If you used gray thin-set then the change of color could turn out to be be permanent. If you used white, then it may fade eventually. The application of an impregnator sealer before the installation is not helping, either, since it will slow-down the curing/drying process.

Wait a few more days before panicking!
Ciao and good luck,