I'm new to blogging and experimenting with your plugin, and I also use Markdown. I'm my only subscriber and this morning I received my first email via your plugin. All seems to work as advertised, except that the email contains the markdown version of the links [here](http://matlabrecipes.com/blah) rather than a hyper link.
The markdown plugin I'm using is: Markdown on Save Improved
which I believe is meant to store the articles as full html, so should in theory be transparent to your plugin. So it is likely an issue with that plugin (I will contact that author) but was wondering if you have you any experience of using Markdown with your plugin? and can recommend a setup etc.