Removing the closing php tag didn’t work. I have narrowed the problem down slightly. The problem existed after installing the ‘Page Links To’ plugin. I have removed the plugin and can’t see any tables it may have created. It is still somehow conflicting with my functions.php file.
The problem was IE dodgey box model I think. I had to remove a div and replace with an absolute. I spent until past 4 in the morning to fix this ?? so annoying.