Hi @bbkr-org, this is due to how OS X's full screen functionality works. You'll see the same when you try putting QuickTime Player videos or even Opera itself or any other application in full screen mode. You can change it by going to System Preferences -> Mission Control and checking "Displays have separate Spaces".
BTW: It works (primary screen is usable) when playing video using Flash, but I want to avoid this technology since I'm not a hipster.
As you've probably guessed by now, this is because Flash doesn't use OS X's full screen mode 🙂