I think the SDK Tool scripts have a Windows related bug. In particular, the command String passed to \SenchaSDKTools-2.0.0-Beta\command\src\Cmd.js is as shown below; note that phantomjs script file name ends with a .bat extension:
phantomjs D:\SenchaSDKTools-2.0.0-Beta\bin\..\scripts\phantomjs-jsb.js.bat --app-entry index.html --project app.jsb3
On Windows, the phantomjs script file on the filesystem is scripts\phantomjs-jsb.js, with no .bat extension.
However, when I modified Cmd.js and hard coded the cmd String to use the correct file/path, a whole different set of bugs appeared.
Don't know if this info is helpful or not, just thought I'd mention it.