I suspect I may be misunderstanding something rather than there actually being a problem with JS Builder... anyway here goes:

When I run it against my js2b file everything goes fine, files are generated and they work great however all my source files are modified (the license text from the jsb2 file is inserted at the top):

 *  License Text
It wouldn't be a problem but this keeps being added repeatedly to the top of my source files everytime i run JS Builder. I've tried leaving the licenseText value blank (licenseText:'') but that doesn't make a difference. Leaving the licenseText property out of the file just produces an error when running JS Bulder.

The top of my jsb2 file looks like this:

    projectName: 'Test App',
    deployDir: 'www',
    licenseText: 'wibble',
    pkgs: [{
Any help would be appreciated.

Also, if anyone is interested I've written a basic VB.Net object for parsing jsb2 files and inserting <script> and <style> tags into pages.