Unfortunately, my recommendation is that you not edit a responsive email at all with the WYSIWYG editor. You should make the changes in the HTML. If you use the WYSIWYG, you'll inevitably have to fix the HTML.
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I'd encourage you to check out Knak. Knak allows Marketers to quickly and easily create responsive Marketo email and landing page templates with no coding required. You can then bring it into Marketo and edit, and everything will remain responsive, no matter how you edit it.
www.knak.io - you can make your first template for free.
We actually figured it out. Marketo was changing the case of a number of our IDs and classes – once we normalized the case (e.g. uppercase/lowercase), it seemed to fix the issue.