A side effect of using the showConsoleWindow option set to false is that it causes JavaFx application windows to start minimized. To me this is unexpected.

The problem seems to be the /min part of the line JAVACMD=start /min javaw. When /min is removed it behaves as expected for both JavaFx and Swing (tested in Java 8u161).

Workaround

In my environmentSetupFileName script, I put set JAVACMD=start javaw.