Thanks for thinking this through with me Jim, I really appreciate it. Looking back I suppose it was a bit lazy on my part assuming the data folder was to blame.
Turns out to be Google Analytics Urchin Module triggering the partial encryption error.
<script src="http://www.google-analytics.com/urchin.js" type="text/javascript">
</script>
<script type="text/javascript">
_uacct="UA-#######-#";
urchinTracker();
</script>
...is what I'm getting in my cart pages generated by SS.
This needs to use the encrypted address instead:
https://ssl.google-analytics.com/urchin.js
Shopsite isn't generating the ssl string in the cart?
I know I can manually add the script to the template pages, but that doesn't fix whats going on here in the SS analytics config panel.