The Joomla 3.2 release updated some jQuery elements, removed more MooTools dependencies and saw the introduction of com_ajax
so you probably experiencing a conflict.
More specifically, you are probably experiencing a JQuery conflict and need to use noconflict()
you can read how to adapt your script to use jQuery in noconflict() mode here
Something as simple as this may work:
// Masonry for boxes
function adjustments() {
var $j = jQuery.noConflict();
$j('#position-2').masonry({
singleMode: false,
columnWidth: 272,
resizeable: true,
itemSelector: '.newsflash-item',
isAnimated: true
});
}