Right I've solved this major pain in the ass!
There was a page in the root of my site /public_html/index.htm
I viewed the source and it was exactly the same source as that of the homepage if I viewed it with the WP Super Cache comments and all the rest of it. The build date was exactly the same as the comments in the site.
I delete this page and now the site is working again!
Finally.
Why this page was cached as static HTML and put in the root of my site I have no idea. The index.php file was there but I guess (just like IIS) that you set a precedence of files to run e.g default.htm, default.asp, index.htm, index.asp etc) and the .htm was top of the list.
The index.php file is the one all the WP code throws everything through with their massive overkill of PHP instead of adding .htaccess rules into the file to handle /tags/, /category/, /post/date/blah etc. If you actually look at the code that has to run on every page load just to work out what kind of rewritten URL it is - then you will CRY! Why not just take the users settings for permalinks and make .htaccess rules for each major branch.
Anyway I digress it seems to work for now and if anyone else has the same problem check for an index.htm file in their root and delete it. Whether Super Cache put it there or not I don't know but it buggered me up for 10 days!