In the doc http://docs.mongodb.org/manual/core/document/ we mention that the timestamp is stored as a time_t in seconds.

We should clarify that while its stored in seconds we display it in milliseconds when output from shell. Under 2.2 the creation of a Timestamp takes a milliseconds value rather than as seconds which impacts how a timestamp is used.

This is also effected by the changes to the constructor outlined in SERVER-7718