Emulator

Game Name?
Any (Wind Waker)

Game ID? (right click the game in the game list, Properties, Info tab)
GZLE01

MD5 Hash? (right click the game in the game list, Properties, Verify tab, Verify Integrity button)
d8e4d45af2032a081a0f446384e9261b

What's the problem? Describe what went wrong.

With render to main window on, exiting fullscreen loses focus and you cannot get focus back by clicking the game window.

(disable background input, use emulated wiimote or standard controller)
Check render to main window
Load a game, (enter) and exit fullscreen
fail to control the game
click game itself
fail to control the game
click outside of the dolphin window and then click the window again OR click anywhere on the dolphin UI itself
control the game

Is the issue present in the latest development version? For future reference, please also write down the version number of the latest development version.
Yes (5.0-10125)

Is the issue present in the latest stable version?
no

If the issue isn't present in the latest stable version, which is the first broken version?

Works as expected on Wx but not qt on 5.0-6137. Likely never worked on qt.

What are your PC specifications? (CPU, GPU, Operating System, more)
Win10 1809
i5-6600k
gtx 1060