_UserException: Attempt to open a database file '...' that is currently in use

I have an application which runs correctly in NetbeansIDE but after building it, it won't just run sometime, the app stop responding to event at a particular point. I was able to reproduce this issue while running the jar file in command line and I got this exception which I have it stack attached here

http://i.stack.imgur.com/IH8XZ.jpg

This I still don't really get how to work around after searching google. However this exception only happen after running the app the second time. If I'm runnig the app the first time after rebooting my system. Everything is ok but after closing the app and rerunning it the this issue occur. The app was built on javafx though

In embedded mode the database cannot be accessed at the same time by more than one process. Make sure that the database file is closed by one run before another attempt to access it by another run, or use client-server mode.