Solved! Go to Solution.
What I usually do is setup a template section in Marketo for my litmus snippet. Then in the Email Designer, double-click the Template section, click the HTML button and paste the code there.
Here are some screencaps from a previous campaigin. The code did work (Check out the results here: https://litmus.com/pub/a/dedecfb )
I've been chatting with Marketo Support about disappearing tags and such. I'll update you if I get some more information!