Good find -- seems i didn't test a new piece of code i added to support language scripts (like .pl perl scripts, etc.)
Try updating or re-downloading, should be fixed now.
For those who care, the new version will create a temporary batch file and run that for you if you specify a script file on the commandline. The bug was being caused because of a combination of the program mistakenly thinking it should make a batch file combined with it not remembering to use the short version of the filename, needed when i shell the batch file. Should be all fixed now.