Emulator Issues #6050
Screen freezes (game still running) when windows 8 warns about program trying to run
When some program tries to run (in my case, Java update checker was the cause both times), Windows 8 will hide what you run full screen, and only show the desktop background and a warning message. After returning to Dolphin's window, the screen no longer updates as the game is playing.
To reproduce, just play fullscreen and wait for Java to pull its usuall shit.
This happened on Dolphin 3.5-402, with Dx9, fullscreen. Only played Metroid Prime PAL GC during this, but I assume it's not game specific.