Ever since Microsoft and IE updated the way flash and other similar apps are embeded things have been a pain on both the server and client side. That was the major starting point, breaking any and all interactive flash pieces on the web. Secondly, Macromedia (Adobe now) decided it would be a good time to release Flash version 8. It has a lot of cool new features, but results in the downside of most people still having version 7 and things not working properly.
There is a decent work around. There is for most programming issues I expect. You can read about it here:http://blog.deconcept.com/swfobject/