OK So I eventually realised this is taken care of by ASP.net themes and there's nothing you can do to change it really without adding exceptions etc..
Since I am not going to be changing themes, I turned themes off in the web.config file and hard coded the CSS links with root relative URLs into my root.master page..
This also means my custom 404 error page now works on all request, even if they have /folders/
thanks :)
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