Loaded up the latest nightly build of 6.0 (Release 6.0.0_BETA1_1295.CentOS5.20090305130954_main CentOS5 FOSS edition), setup an account with "pop-up notifications", installed Yahoo BrowserPlus, and this is the screen I get when I should be getting a notification:

I can't select something to allow/deny, and I have to end the firefox.exe process to make the box go away. Any ideas?