At the beginning of a season, or at the beginning of a run of episodes, Matt and Trey meet with the other South Park writers to brainstorm ideas and pitch story lines. For example, at the start of the fourth season they came back from a retreat with ideas and outlines for the first four episodes, the titles of which would end with the tag "2000" (e.g. "Cartman's Silly Hate Crime 2000"). As script was delivered to the Storyboard and Production departments, they were given an episode number, #401. From that point on, everything associated with the episode (Corels, storyboards, temp lead sheets, audio, purchase orders, billing, etc...) has to have the same number, changing it midstream would just confuse everyone. So even though #402 "The Tooth Fairy's Tats 2000" launched the fourth season, "Hate Crime 2000" kept the #401 tag.
Stay tuned for part two of this increasingly convoluted answer, coming soon!