This is not to say that the NSA was aware of linear crypto analysis when they made their recomendation. Indeed the fact that their s-boxes also happened to be just good enough to beet differential, and the fact that an independent government investigation (the details of which are classified) cleared them of wrongdoing, are enough to convince that they did not intend to introduce a hole. Furthermore, the NSA has also now published the requirements they used to generate their s-boxes. Schneier suggests in his book that the s-boxes were weakened unintentionally by the act of introducing structure to them, without knowing to defend against linear analysis.
[1] Bruce Schneier, Applied Cryptography
Was that the result of the last-minute "black box" change? I never heard the result of that, so any light you shed would be welcome.
You can read more about their involvement here: http://crypto.stackexchange.com/questions/16/how-were-the-de...
Thanks for the pointer.