I seem to have found a fix.
In the engine_config.txt file I changed sound_device from 0 to 1. So far it works, but the sound option in the options menu seems to start with the wrong selected sound, meaning I need to change it everytime.
Obviously the daisy chaining had nothing to do with it, but I did knock off the HD Audio motherboard cable while re-jigging it. Perhaps plugging it in again messed things up? No other games were affected though.
I guess this can be classed as 'resolved' now, although obviously not ideal.