You might want to update to the latest version of Jython. This one works just fine on my Windows7 machine ...
run a batch file using Jython
The Windows batch file 'hello.bat' is:
echo Hello, from batch file
tested with jython2.5.2
In my experience most of my normal Python26 code seems to work with Jython 2.5.2 as well. Jython is actually a real nice way for Java programmers to enjoy Python syntax, and for Python programmers to get used to a little Java.