I have Beta 3 and get the same results. The output is just black lines and the resultant .jsb3 file has an empty file list. No errors anywhere and running the app.html in the browser produces a good view.

{
"projectName": "Project Name",
"licenseText": "Copyright(c) 2012 Company Name",
"builds": [
{
"name": "All Classes",
"target": "all-classes.js",
"options": {
"debug": true
},
"files": []
},
{
"name": "Application - Production",
"target": "app-all.js",
"compress": true,
"files": [
{
"path": "",
"name": "all-classes.js"
},
{
"path": "",
"name": "app.js"
}
]
}
],
"resources": []
}