I just noticed this: Markdown style hyperlinks don't work when the text content in the principal text area has HTML. For example, when you moderate->close a post and then try editing the moderation comment to add links, the edit brings up a page with the content already populated with html tags (such as the <p> tag).
I got the links working once the tags were removed. I think the Markdown parser gets into a conflict with a different HTML parser and that's what causes this. Any thoughts on how we can address this?