Yes, its all to do with the Windows update KB3140743 - it included a new driver set for USB input devices. It has completely screwed up GTA5 controller/keyboard interactions to the point of Online play and gameplay recording just does not work (because I need to press certain keys to type in-game text, and to also start/stop ShadowPlay recording).
Its a nightmare, but I've only found it affecting GTA5 so far, although I did notice odd USB device issues in Elite:Dangerous too. Going to investigate further tonight.