Just to update others, this problem is still ongoing, although the menu worked fine on the article page, Joomla standard search module would stop mootools adding the script code into the page, which froze the menu.
I have not had much luck from admin or tech support. Tech support has currently inadvertently disabled our company navigation menu on a live website for 4 hours+ (not happy at all potentially costing the company thousands
)
does any other super coders out there have a solution to this bug with Mega Menus?