WordPress Text Flow vs. Markdown
Michel Fortin reviewed his analysis in how to make PHP Markdown works with WordPress.
It works since a year now, but there have always been many glitches. All this relates to the text flow model WordPress has adopted, which is very powerful but badly adapted to a writing syntax different from HTML. To work correctly, the Markdown plugin must in some way mess with the inner working of WordPress by moving many filters out the way.

