X360 Controller Unresponsive Ingame

[Latias420]

I've been using dolphin for about less than a week so far, and it's been performing fine, but I leave it for a day, and I come back to play without having changed any settings and when I go to play, nothing I do on the X350 controller works in game, but on the configuration screen it registers any inputs.  I've no clue why its acting like this, as it has worked fine in other emulators/games, some help would be really appreciated

[ExtremeDude2]

What game are you playing and what are your settings?

[Latias420]

I'm playing both F-Zero GX and TLOZ: Wind Waker, with all of the default settings on Dolphin as it came minus controller bindings