This may be exactly the way it’s supposed to work but it confused the
crud
out of me so I thought I’d post for the few non ubergeeks in the
audience
like myself.
If you turn on the ‘Visual Rich Editor’ in your settings, but use a
client
like TextMate’s blogging bundle to compose your posts with Markdown and
then
edit them later from the web interface, you will lose. Hard. the
Visual
Rich editor will interpret your Markdown as plain text, try to add HTML
tags
into the budy of your article and generally mark things up as if you
were
typing them in from scratch, resulting in a big old mess 
The moral of this story is: If you use external clients and Markdown (or
ostensibly any other text filter) turn off the Visual Rich Editor.
-Chris