There are two bugs in the Skein code. They are subtle and esoteric, but they're there. We have revised both the reference and optimized code -- and provided new test vectors. A revision of the paper -- Version 1.1 -- has new IVs, new test vectors, and also fixes a few typos in the paper. There is also a revised version of the NIST submission CD.
Errata: Version 1.1 of the paper, reference, and optimized code corrects an error in which the length of the configuration string was passed in as the size of the internal block (256 bits for Skein-256, 512 for Skein-512, and 1024 for Skein-1024), instead of a constant 256 bits for all three sizes. This error has no cryptographic significance, but affected the test vectors and the initialization values. The revised code also fixes a bug in the MAC mode key processing. This bug does not affect the NIST submission in any way.