SOLVED: OK! Skip all that confusion above, and here’s some tips:
A couple of things were going on here. To begin with, there was a base tag set on each page:
<base href="[(site_url)]" />
This was being set to the domain name without the www. prefix, and so any time the site was accessed with the www, jquery tried to go cross domain with its ajax. Without realizing this, I made a rewrite rule to remove the www, which worked for a little while and then stopped.
This was because of the fact that snippets like such as navigation were cached ([[ ]] brackets rather than [! !]) causing links on the navigation to mess with the subdomain unexpectedly.
Now that it works, its all good, but another solution might be to just change or remove the base tag.
