Hi Peter--when I use media queries in Marketo email I make sure to include them in the template--I don't try to bring them in using the WYSIWYG editor. (It sounds like that's maybe what you're doing?)
If it's not worth creating another template and you only want it for this particular communication, you could also download the HTML from the email you're working on, add the media queries and styles into the head section, then import it back into Marketo by replacing the HTML in the email you're working on.
Here's instructions on downloading/replacing: http://community.marketo.com/MarketoTutorial?id=kA250000000Kz3WCAS