Even though it is a runnable jar, you can still run it from a console -- open a terminal window, navigate to the directory containing the jar, and enter "java -jar yourJar.jar". It will run in that terminal window, and sysout and syserr output will appear there, including stack traces from uncaught exceptions. Be sure to have your debug set to true when you compile. And good luck.
Just thought of something else -- if you're on Win7, it often has permission problems with user applications writing files to specific directories. Make sure the directory to which you are writing your output file is one for which you have permissions.
In a future project, if it's big enough, you can use one of the standard logging facilities for 'debug' output; then it will be easy(ier) to redirect it to a file instead of depending on having a console. But for a smaller job like this, this should be fine.