Emulator

What's the problem? Describe what went wrong in few words.

With Background Input disabled, you're unable to use the controller at all if you do not have the main window or game window active.

What did you expect to happen instead?

Controller input to work without background input and not being focused on the main window.

What steps will reproduce the problem?

1. If Background Input is enabled, disable it.
2. Start any game.
3. Take focus off Dolphin.
4. Attempt to use the controller.

Dolphin 3.5 and 3.5-367 are old versions of Dolphin that have
known issues and bugs, so don't report issues about them and test the
latest Dolphin version first.
Which versions of Dolphin did you test on?
4.0-7099, 4.0-6959, 4.0-1904, 3.5-1749

Does using an older version of Dolphin solve your issue? If yes, which
versions of Dolphin used to work?

No

What are your PC specifications? (including, but not limited to: Operating
System, CPU and GPU)

OS: Windows 8.1
CPU: Intel Core i5-4670k
GPU: NVIDIA GeForce 760
RAM: 8GB