I want to make this guide as a word of warning to anyone new starting the game. DO NOT leave it as your last achievement in the game. What happened to me, I got 100%, the achievement "unlocked" and didn't seem to sync to live. After rebooting my PC, I saw the achievement had relocked itself and my save had corrupted.
My suggestion would be to leave one or two achievements (such as the catch a batarang and the glide for 100m) to unlock afterwards in the case that the achievement doesn't sync correctly.