This sounds familiar. Brent Pedersen recently pointed me to this link when I was troubleshooting a similar problem:
http://jakeo.org/blog/2007/03/16/css-opacity-and-flash-transparency-in-mac-firefox/ Mike
When I load content into a div from an ajax call, the flash movie contained in updated code doesn't display in FF 2.0.0.4 on the MAC. However it does look as though the movie is there because if I right mouse click on the space it is supposed to be, the flash dialog appears.