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I have downloaded JK and I cannot fathom how to install mysteries of the sith.
Mysteries of the Sith is a separate download from the DF2 main game. While you buy them both in one package, they appear as two games in your library.
I just refreshed my account, as it is described here:

Then, MotS should ve visible in your library and Galaxy, as well.
Post edited March 03, 2016 by Locutus