Last Oct. 2, former Clinton national security adviser Samuel R. "Sandy" Berger stayed huddled over papers at the National Archives until 8 p.m. What he did not know as he labored through that long Thursday was that the same Archives employees who were solicitously retrieving documents for him were also watching their important visitor with a suspicious eye. After Berger's previous visit, in September, Archives officials believed documents were missing. This time, they specially coded the papers to more easily tell whether some went missing, said government officials and legal sources familiar with the case. The notion of one of...