SP2 includes a pop-up blocker integrated into IE. The "pop" sound you describe sounds like the new IE sound when a pop-up is blocked. I get the pop sound but none of the other symptoms you describe. Instead there's a new blocker toolbar (just below the address bar) that opens when a popup is blocked to inform me that it's working.

Do you get any context menus regarding pop-up blocker settings when you mouseover or right-click the indication in the lower right corner that you're describing? I