The Doxia Markdown module currently uses the Pegdown module to generate HTML and then relies on the Doxia xhtml module to parse that. The Pegdown HTML generation currently produces HTML that doesn't exactly match what other modules produce, which causes some style errors. Specifically, for "code" blocks, there is no wrapping <div class="source"/> wrapper, which causes output to look strange. The attached patch adjusts the output.
Of course, if the markdown module is going to be refactored to produce actual Doxia AST events, that might make this less of an issue. But I still think it'd be good to commit this patch in the meantime, especially if 1.3 is released before the refactoring.