Okay stick with me on this one. It's not that complicated.
What happened is that the director put together one cut originally for the movie, or it may have been that the cut was a collaboration between the director and some other mysterious "cutter" - the editor perhaps? This was the cut that got put out in 2001, and it bombed. No one knows why for sure. Equally unexplained, the movie gained a belated but pretty devoted following on either Netflix, DVD, Laserdisc or Blueray, or perhaps Broadcast or Cable Television - whatever the technological equivalent of "watching a movie at home" was, during this time period. People got into it and dug it that way, at home, so in 2004 a six-foot tall magic rabbit went back in time, gathered all the original footage plus some footage that had been "lost" (or perhaps, "cut"), and this was compiled together, again without explanation, for release once again to theaters as The "Directors Cut."
That's what really happened, but the irony is you still don't really know for sure what exactly the deal was with that rabbit. You might have to admit it's a little unsettling.