Probably, it is due to permissions - when the app starts there is no user logged in, and the app does not have permission to access the file. When you run it manually, it gets it's permissions from your user ID and can work with it fine.
Try changing the file (and the folder it is in) permissions so that anyone can read and write it.
Or run the app as a specific user - google can probably help there:
http://www.google.co.uk/search?sourceid=chrome&ie=UTF-8&q=execute+app+as+user[
^] (I've never tried to do it, so I can't be sure how)