After installing the Firefox beta, it seems like it picks up your existing flash player install if you had it set up with Firefox 2. All is not well, though. There must be a few files or settings that don't migrate perfectly.
I didn't notice it at first because the debug output for me was still working. It wasn't until I started working with some rollOver effects that things seemed strange. The rollover event wouldn't fire on a component unless I first clicked it.
Not to worry. If you've installed the flex 3 beta, you should have a player distribution included in your Adobe Flex Builder 3 Plug-in directory (I'm not sure where it is in the standalone install, but it's probably similar). In there, on my mac, there is a player directory, a mac directory and a few flash Player install files. I simply launched the "Install Flash Player 9 UB.dmg" file, ran through the process and tried again. Everything seems back to normal now.