Weird monitor issue in Dolphin

Hi, I'm using the latest Beta build of Dolphin (x64) and I get this weird monitor issue. I am using a duplicate monitor set up. When you run a game in full screen mode, it will run correctly on one monitor, but won't refresh on the other. If you mouse over the game from the taskbar, you can see it refreshing normally, and you can always hear it, so I know its working in the background. But, if you bring it to the front, it freezes in whatever frame it was at. Sometimes, if I get it to display full screen, but still have it in the background (i.e. the Windows taskbar is technically at the front, and the fullscreen Dolphin emulation is in the background but still maximized) you can play it normally and everything refreshes. It only freezes when it is at the front.

I've seen the same thing happen with Retroarch. If I set it to fullscreen mode, and leave windowed full screen on, it does the same thing. If I set it to full screen mode and turn off windowed full screen, it works on both monitors. I'm not sure how I would set similar options in Dolphin though.

Having it behave this way is fine actually, but I don't know how to change the "dominant" monitor (i.e. the monitor that it will work on in full screen). If I could change that, I'd be fine as I only really play games on one of these monitors.

Any ideas what is going on here and how to change this behavior?