Initially seemed a bit odd that a Windows audio configuration issue would affect only one source, but I suppose Windows is only messing with the first pair of inputs, and that's where the Korg is.
I can't fully explain the behavior or recommend a fix other than to agree with daudio that you shouldn't let Windows use the FocusRite.
It's not uncommon for people to recommend disabling the onboard sound in a DAW PC, but I always advocate the opposite: leave onboard sound enabled, and assign it as the Default Device for Windows to be used by browsers, Media Player and other generic multimedia apps. This will keep Windows' mitts off your audio interface. I've always configured my DAW that way and never had a problem. I also use an external mixer so the output of the onboard sound can play through my monitors when I want it to.