You still need to add the path to the executable jython.bat to your PATH environment variable. Here as an example I'm providing my ini-jython.bat, which I use before executing my jython project (in this case it's a Django on Jython project, you can safely ignore the Django stuff, or adapt it to your needs):
set JYTHON_HOME=c:\tools\jython2.5.2
set PATH=%JYTHON_HOME%\bin;%PATH%
set CLASSPATH=dep1;dep1/lib/*;_lib/*
set JYTHONPATH=.;..\django-debug-toolbar;..\django-common
set DJANGO_SETTINGS_MODULE=site_projname.settings
set PYTHONPATH=%JYTHONPATH%
set manage=jython c:\tools\jython2.5.2\bin\django-admin.py
set makemessages=django-admin makemessages --extension html,py
set compilemessages=django-admin compilemessages