Found a solution after much brain-wracking. Instead of this:
<!--[if mso]><v:shape>...</v:shape><![endif]-->
<!--[if !mso]>[fallback goes here]<![endif]-->
This works very well:
<!--[if mso]>
<v:shape>...</v:shape>
<div style="width:0px; height:0px; overflow:hidden; display:none; visibility:hidden; mso-hide:all;">
<![endif]-->
[fallback goes here]
<!--[if mso]></div><![endif]-->
All it does is wrap the fallback in an invisible div in MSO, and deploys the vector solution instead.
Hope this helps someone in the future!