I have found the solution.
I have no idea how WP Super Cache put the file into the root of my site but it created a hardcoded .html file called index.htm under public_html/index.htm
I am guessing just like IIS Apache has some sort of priority where it runs certain file names first before others e.g
index.htm
index.html
index.php
Or something similar.
Once I deleted this hardcoded file from my root everything started working again fine.
I have no idea how WP Super Cache put it there at 7am on the 20th (a day I was in bed with a hangover) and I have never manually copied the generated source, created a file and copied it up to the site.
Maybe a check for this would be good. OR maybe it's some feature I don't know about e.g Stephen Fry Lockdown mode for homepage etc. Not that I ever turn it on.
I just thought I would pass this on.