Subsite in folder – CSS not combining into http body

Hi guys

Sorry to be a pain, i am very close to launch. But i have another question/issue i’ve just noticed. (hopefully its quick)

Using a multi-site network with a folder installation. I have Minify set to on for HTML/JS/CSS and using a CDN. (both minify and combine)

On the main sites (with their own domains in the staging folder) everything works. JS and CSS combined/minified and the CSS is embedded into the HTTP body of the page. So in the Chrome inspector, you cannot see any CSS being loading in the Network Tab.

However, in two of the sub-sites (in folders off the primary domain) that are installed one folder down from the domain root (ignoring the staging folder). All of the CSS files are being loaded in the network tab of the chrome inspector, when they shouldn’t.

Staging site Structure:
Sites that are fine: (primary site on the network -> domain-site-1.com)

domain-site-1.com/staging-three/ (primary site)
domain-site-2.com/staging-three/
domain-site-3.com/staging-three/
domain-site-4.com/staging-three/

Sub-sites that don’t work properly:

domain-site-1.com/staging-three/essentials
domain-site-1.com/staging-three/learning-development

Is this a setting I’ve missed? ie Page Cache > Cache alias hostnames – as i have added all the domains here, but not for the two folder subsites (off the main domain).

Or is there another setting i’ve missed.

Please advise.
Thanks