I am running the following command to get my encrypted obb file for apk expansion.
jobb -d /home/manoj/Desktop/Test -o main.1.com.example.helloworld.obb -k \
I was getting the same behaviour but this was only in a test directory structure I was experimenting with. It had almost no content so maybe this is an issue with jobb at these small sizes. Or maybe some error conditions are met depending on the space taken up by the all the files. I've commented in more detail on the Google Code issue.
I wonder if adding a couple of redundant files might avoid this error behaviour for those that are experiencing it with non-trivial directory structures.