That is an indication that the difference is either with your OS (which it probably isn't) or some part of the configuration specific to your application. At this point I would recommend that you run Sencha Command with the debug flag and see if anything stands out in the resulting output.
Look in the output for strings such as "error" ,"warning", and "FileNotFound".
sencha --debug app build package
Also assuming you have this project in source control, compare anything currently showing as different in your copy with what is currently in the repository.
Something is different and/or wrong, the difficulty is with finding what.