Hi everyone,
I finally have an answer for you. The investigation was successful and we identified the issue:
The final "I'm the boss" achievement was not expected to be implemented in the PC version.
It was a PS3 achievement (hence the "Collect all the trophies" description for it) that was taken into the PC version erroneously. "I'm the boss" was checking for the 45 PS3 trophies of the game instead of Steam achievements, which means nobody was ever able to achieve it on PC.
As a consequence, this achievement was removed and there are now only 45 achievements for Of Orcs and Men. If you have all of these, your profile will display 100% of completion.
We apologize for the inconvenience.