I had the same problem. I solved it as follows:
1. I took out the box with the collector's edition game and installed it from the disc.
2. The game and Uplay automatically patched to version 1.8.
3. I manually patched it to version 2.1.1.
4. I logged in with my account, and all the expansions (including Shades of Darkness and the DLC), all the progress - everything appeared.
Before that, I tried installing it from the electronic version installers - there were the same glitches - English font, the key didn't work, etc.
Thank you! It helped. I downloaded the game without a crack and installed it.