WordPress can truncate Markdown
Here’s a heads-up for Markdown users.
Looking through my Categories and Archives views, I was startled to see raw, unconverted Markdown syntax in certain posts.
What happens in Categories and Archives views, is that posts are truncated to give readers an easy-to-scan excerpt. When this excerpt cuts Markdown syntax in two—or cuts it off altogether—the Markdown processor can’t convert the syntax fully.
The biggest victim is Markdown’s reference style links, which work like footnotes, putting the link information at the bottom of the post; these tend to get cut off. So until the WordPress crew fixes things (maybe with WP 1.5.1?), I’ve gone back to in-line linking.