This is going back a ways... Schneier discusses SKIPJACK at Declassifying Skipjack. Schneier offers a link to a reference implementation at ftp://ftp.funet.fi/pub/crypt/cryptography/symmetric/skipjack (it is still alive). The unoptimized reference implementation is written by Panu Rissanen.
NIST provides the SKIPJACK test vectors in SP800-17, Table 6, pp. 140-42. NIST withdrew the the encryption specification, but left the decryption information and test vectors for interoping with legacy systems.
What I find is the reference implementation and NIST implementation differ. Rissanen's code does not arrive at a NIST Known Answer for the KAT's offered by NIST.
I'm trying to understand why Rissanen's code is not conforming to the NIST KATs. My question is, what is the history of SKIPJACK back then? Did the algorithm have several variants?