I have experienced that too - everything was correct in the settings, but no audio in, and the waterfall had frozen, but the clock was still going.
I think it may be linked with another problem I have where there is no modulation out from WSJT-X to the rig. Sometimes halting and restarting the TX fixes it, sometimes I need to restart the program. my suspicion is that Win 10 is messing up the audio ports as I once saw the audio out going to one of the other audio channels watching which was receiving audio in Sounds. This was despite all the audio settings being correct in wsjt-x settings and in the sounds properties for apps in win 10.