sounds like your application is looking for its data file in a place where it can't find it, and you've programmed it to silently swallow the errors that causes.
Yep, 9/10 times the issue description matches "Works when running through Netbeans, not when running without it", there are either absolute paths in the code, or even worse relative paths that are based on the assumption that Java looks for files in My Documents.
Yes, it's right, an application can't find it, my application has a modal-dialog window with error message, like - e.getMessage() will show - "can't find C:\Users\user1\...\Desktop\contacts.xml". And when I run an application it showed the modal-dialog. I think I need to make some mechanism to set absolute path to .xml from my project, not from my OS. Could you tell me please some tool or mechanism, how I can fix it?