That is odd!
I am running Safari for windows 4.0 (530.17) and it works fine. Menu is over the top of the flash as it is supposed to be.
And I just fired up my mac, that I use for testing, and it looks good there too.
mac os 10.5.7 Safari 3.23
Although in FF, its not working now. That is likely due to removing the second instance of the wmode parameter. I think that one was there for non ie browsers