The achievement text says you need to fill out the map, but this isn't doable until you're close to beating the game.
You must have 95% Map Completion by the time you reach the last save point; the small room before the final boss where Mr. Hyde / Russell Crowe gives you a pep talk will count as 1%, and the last 4% will be filled out during the final fight (four squares in the map) and during your escape after defeating the boss. This achievement will not pop until the end credits finish rolling and you see your final game stats.
If you beat the game and you didn't get 100% Map Discovered, you missed a room somewhere. Reload your save and make sure there are no dark spots in the map, and compare it to the map posted in the Steam Guides to double check.