Nobody should be using the original script, and unfortunately many of the other implementations out there are direct transliterations that replicate all of its absurd errors, like where if you mention the MD5 hash of another token in the document, the hash will be replaced with the token, because it uses that as an inline escaping mechanism! Reddit got hit with a XSS virus that got through their filters because of it: http://blog.reddit.com/2009/09/we-had-some-bugs-and-it-hurt-...
See the changelog for what started as a PHP transliteration and turned into a rewrite that squashed 125 (!) unacknowledged bugs: http://michelf.com/projects/php-markdown/
The worst part is that he outright refuses to either disclaim or fix his implementation, and so far he's repudiated everyone else's attempts to do so. He's a terrible programmer and a worse maintainer, he really still thinks the documentation on his site is comprehensive and canonical. As much as Jeff Atwood leaps at every chance to play the fool, there's no way his directorship can be anything but an improvement.