Most recently, I went in to look at settings after disconnecting from a QSO. The window displayed properly, and I closed it (I think, by the usual method of clicking of the red X, but I'm not sure). After that, VarAC continued to run, but the program was totally unresponsive to any keyboard or mouse input.
I regained control by right clicking on the task bar and noticed the settings window still was active. Once I closed it (right click, then "close window") I was able to re-start VarAC, VARA-HF, etc.