It seems WinPython has chosen to use the environment variable name HOME to point to its settings folder (HOME=c::\WinPython-31090\settings in my Win10 installation). It doesn't require much imagination to see how using such a generic variable name is asking for trouble with respect to other applications that unfortunately chose to do the same thing (CadSoft's EAGLE, in my case.)

If it's feasible to revisit this decision, I'd suggest either using the existing $HOMEPATH variable (e.g., $HOMEPATH\WinPython\settings) or creating a WINPYHOME or similar environment variable for your own use.