I'll admit that I was another kid who heard it on Shrek and snagged the song. And I think Rufus Wainwright does the song justice. (The Cale lyrics still make sense to me.)
But I came across the original Cohen and Buckley's cover while searching for the lyrics, and I kept running into about six different iterations. At the time I chalked it up to people on lyrics boards mishearing words (which happens all the time) but now knowing better, I enjoy almost all the versions.
I just happen to enjoy the Wainwright one a little more--particularly since it came into my life at a time when the lyrics made sense for me personally.