enigma1 - 11:05 am on Apr 1, 2012 (gmt 0)

you hook the top html for the click event to close the menu
$('html').click(function(e) {
// Add conditionals and close menu here
});

and you prevent any event propagation of the menu container to the parent handlers so they're not notified since you handle clicks inside the menu container (so the previous code - above won't be informed to close whatever you need to close.
$('#menu').click(function(e) {
e.stopPropagation();
});