Geoff Stearns has released an update to SWFObject (formerly known as FlashObject) to fix a bug in the way IE 5 and 6 display Flash. IE 7 is not affected. The issue only appears if using Flash Media Server (aka Communications Server). If you refresh the browser when a swf is playing, the Flash audio continues playing to the end or until the browser is closed.
Further information and a new version of SWFObject can be found here.
-rG

