Fallout 3 is the exception to that rule. NO achievements are blocked in fallout 3 with cheating.
And if the Achievement Unlocked box popped up then the achievement was glitched. happens rarely but does happen.
try to load a save right before you finished the quest and redo it. or use the unlock achievement cheat.
That's odd, because the only 3 achievements I got in FO3 were when I had no cheats active.
For example, I have the "Big Trouble in Big Town" achievement, but not the "Escape" achievement. I've completed the entire main story line and got no further achievements apart from the three I got near the start.
I know the later ones I wouldn't have got because I disabled GFWL so it wouldn't interfere with the trainer but I played a good third of the game with it active.
Maybe I'll try restarting the game from scratch and and see what happens...