[Plugin: W3 Total Cache] CDN Origin permalinks issue

I have an issue similar to this:
http://ww.wp.xz.cn/support/topic/plugin-w3-total-cache-cdn-origin-setting-doesnt-modify-permalinks?replies=8

This scenario of wanting to CDN the whole site is valid.
For example, I want to CDN the whole site to a server in an alternative global datacenter to hopefully speed up connections in that proximity.

I have it 95% working as required, but whereas the user in the post could not get permalinks to work at the CDN URL, I seem to have it working for some URLs and not others.

For example, in my WordPress navigation menu, some permalinks DO point to the CDN URL and some don’t.

Where in the W3 Total Cache code would this filtering be happening so I can try to debug it?

http://ww.wp.xz.cn/extend/plugins/w3-total-cache/