CKEditor 4.2 and Media Module, Has anyone gotten this to work?
CKEditor 4.1 introduced a feature called Advanced Content Filter. It might be stripping some code. You can test if it's the cause by adding this code your ckeditor/config.js file:

CKEDITOR.config.allowedContent = true


Granted, you shouldn't just leave it true, but it will give you an idea if that's the problem.