When the DOM is first built, some of the attributes affect properties on the element, but then changing those properties doesn't always modify the attributes again.
Take a look at this example: http://jsfiddle.net/AzDfx/ So, MooTools tries to take care of that for you. If you were to call $('me').get('checked'), it would correctly check the property on the object, since it knows the "checked" value works like that. In short, just always use .set and .get.
