There seem to be many types of issues being discussed on Steam’s game discussion page.
Ubisoft responded trying to assure players that they are working to correct the issues and that “None of your content is lost and will reappear once this work has been carried out.”
The forum post continued, “Those with issues with keys, these are not broken and will be fixed as soon as possible. Steam users: if you see Shades of Darkness in your list you are correctly updated. Please ensure you restart Steam. Those with a new purchase of Standard, Gold, Deluxe Editions: we are aware of a menu issue and are working to correct this.”
Here is a forum post recommended by Ubisoft until the issue is fixed – Thread: How to CORRECTLY patch to 2.1 AND install Shades of Darkness.
Have you experienced any of these issues?