Many have noticed that as of Joomla 3, your elements with jQuery tooltips will disappear after you mouseover them. This is caused by a conflict with Mootools. If you check the pages where you are seeing this issue, it's when Joomla's Mootools is loaded. The fix is simple:
jQuery(document).ready(function($) {
$('.hasTooltip').each(function(){this.show = null; this.hide = null;});
});
This will disable the hide behavior for Mootools' tooltips, which is declared the same way as jQuery's. You can replace $('.hasTooltip') with whatever class you are using for your tooltips.
Hope this helps!