Yep, under Content Management -> pages, on the root page -> master page tab, there are a few paces I can enter html. The section that is still in the head tags is where I've added a script tag.
After this has been saved I can see this when I view source only if I'm not in preview mode.
On the root page In the general tab I've set "use cache output" to no, "allow file system cache" no and clicked "clear output cache" and saved the page.
In Debug I cleared the cache and I've gone to System, clearing unused memory, performance counters, cache and restarted the application.
In IIS I've stopped the site, restarted the app pool, started the site and cleared my browser cache and in preview mode that content still won't show. I've tested in other browsers too, in all of them it's only broken in preview mode.