There is finally some news from the Ubi folks about the problems people have been experiencing. Also, the official page lists up a set of installation instructions depending on which version you have:

"Maintenance is now over and missing content issues have been solved.
Yesterday, the Heroes VI standalone Shades of Darkness was officially released.
We have decided to take advantage of this opportunity to fix several existing bugs in all Heroes VI versions..
However some user experience difficulties have appeared with the auto patching system. In order to fix this issue, we strongly recommend you to get the 2.1 version and follow this tutorial.
The music and voice bugs have now been fixed with the Steam version. You may have to restart Steam to get the update.

Regarding issues related to missing content:
- Game not displayed on the Uplay platform (“My Games”).
- Unable to play multiplayer maps & locked campaigns, maps, bonuses etc (servers maintenance will take place in the afternoon in order to fix these issues).

We are currently working to solve these problems and will update you throughout the day with further information. "