My program crashed when I tried to add a watch to the home directory of my Ubuntu install (/home/username/). The likely cause is that JNotify is sent into an infinite loop due to some symlinks in that folder (most prominently the /home/username/.wine folder). I'd therefore suggest excluding folder symlinks from watching, or adding an extra method parameter that allows disabling the symlink watching.
I submitted a patch for this here:
https://sourceforge.net/tracker/?func=detail&aid=3604731&group_id=154048&atid=790220