I installed safari 4 on one of our IBM XPs and the menu is on top.
I uninstalled safari 4 and reinstalled it on this HP Vista machine and it still had the flash on top. I uninstalled 4 and reinstalled 3.2.3 and it works fine so its something between HP - Vista - and the safari 4 install.
Do you have a Vista machine that Safari 4 has the menu on top. It would be nice to know that this issue is strickly on this machine. I don't have any other Vistas to install it on.