I followed the advice given here http://www.inkthemes.com/community/threads/update-to-1-8.7503/#post-27904 to the letter and v1.8 has completely lost the menu structure, revert back to 1.7.9 and all is well again. cache was cleared each time so what has gone wrong?
Found the problem, it had lost the check box setting for which main menu to use. It probably wouldn't have happened if it was updated via the admin area.
