NSA (partially) Declassified
Lally Singh writes "Posted yesterday on the National Security Archives was the NSA's "Transition 2001" report, prepared as an introductory report for President Bush (II)'s incoming administration. "The largest U.S. spy agency warned the incoming Bush administration in its 'Transition 2001' report that the Information Age required rethinking the policies and authorities that kept the National Security Agency in compliance with the Constitution's 4th Amendment prohibition on 'unreasonable searches and seizures' without warrant and 'probable cause,' according to an updated briefing book of declassified NSA documents posted today on the World Wide Web.""
The derivation of the S-Boxes are a secret. Changing the numbers in the S-Boxes certainly weaken DES, but it is not published as to _why_ the ones the NSA picked are so strong and how they were derived.
Did you actually study cryptography, or are just quoting some book about spies? There is nothing mysterious about S-Boxes in DES, they are resistant to differential cryptanalysis (with 4th S-Box being still rather weak, IIRC), but that's about it.