Without a script to replicate the problem anything I tell you from here on in is conjecture. For example, you may experience weirdness if you're running system commands in an environment which has problems.

From experience it's best that we don't draw this out piecemeal. Don't introduce new factors to the equation (e.g. MS Windows build), stick with the facts and provide an example which anyone can run to try and recreate the issue in question. I say 'try' because if this problem relates to an issue with your environment you will need to debug the issue further. For clarity, on the target system running the packaged version throws an error, running the normal version does not? My advice for your next post would be to include the example code discussed and details of the environment you're running this in.