The President’s order commuting Rabbi Rubashkin’s sentence was definitely issued and even became publicly available on Zos Chanukah (in both Washington, where it was issued, and in New York, where R. Rubashkin was). I believe he was driven out of jail either before shkia or bein hashmosos.
It’s amazing that he was released within hours of the presidential commutation, on the very same day. Virtually always in the case of a pardon or commutation it takes at least days if not weeks for the prison system to process the release.