Looks like i have a fix for this and a better understanding of why this is happening.
It is to do with the permalinks being set to anything other than default and relative paths. As this changes the actual url of the pages the script doesnt execute correctly.
The fix i have found is to add <base href=”<?php echo get_option(‘siteurl’);?>” /> to the bottom of the header.php file.
Hope this helps someone out.