What kind of controller do you have? I know some controllers (e.g. Logitech F310 and its family) have physical switches to change from Xinput to DirectInput. I remember some people having trouble because it was set to DirectInput.
If you have any Wii games (or WiiWare) do those work? That is to say, is this problematic for just GC games or everything in Dolphin?
Other than that, maybe try enabling Background Input. Might be possible that Dolphin is losing focus. Not sure how that would happen, but it's worth seeing if it has any effect.
If you have any Wii games (or WiiWare) do those work? That is to say, is this problematic for just GC games or everything in Dolphin?
Other than that, maybe try enabling Background Input. Might be possible that Dolphin is losing focus. Not sure how that would happen, but it's worth seeing if it has any effect.