The permutations in DES have nothing to do with security; there is an excellent explanation by Thomas Pornin on what their purpose was: http://crypto.stackexchange.com/a/6/592
What was altered were the 8 S-boxes, seemingly random lookup tables that map 6- to 4-bit values. More details by Don Coppersmith himself at: http://simson.net/ref/1994/coppersmith94.pdf
I phrased that poorly (and just edited my first sentence to reflect your correction). What I was trying to add was that the NSA made some other modifications to DES that were also seen as dubious at the time.
What was altered were the 8 S-boxes, seemingly random lookup tables that map 6- to 4-bit values. More details by Don Coppersmith himself at: http://simson.net/ref/1994/coppersmith94.pdf