In SharePoint 2010 if CMSSiteManager.js library is loaded besides jQuery, then much of stuff stops working. The reason is that the dollar sign ($) is used in cmssitemanager.js as well which conflicts with jQuery. Mostly it appears on pages where you load jQuery and have an image library with thumbnails. To avoid this, just replace all $ with jQuery in your custom scripts. A more crazy situation is when avoiding $ isn’t enough.