Diablo 3 launched to a bit of a snag, as a massive glut of players led to overloaded servers and network problems. While those issues seem mostly resolved, some users are reporting missing Achievements as well.
An extensive Blizzard forum post has several users complaining about missing achievements. A reply from the QA department attributes this to server issues. "The achievements server in particular is being hammered, which may be why your achievements are not showing up," he said. "It is not that they are deleted, but that there is a (very long) delay in retrieving that data." Blizzard is said to be working on the problem.
Players are still complaining about missing achievements, and some users have still reported server problems in general today. If your achievements are MIA, though, it sounds like the game still remembers what you've accomplished and you'll get them all back once the servers are a bit less overloaded.