Here is image how sometimes it looks on Ubuntu:
http://a.wieza.iq.pl/media/filewindow.jpg
Notice that the file pane is sometimes 1 pixels wide (and sometimes normal, every time it openes it has different width for some reason, maybe depends on what was shown before). This makes it sometimes look like there are no files when you enter a folder because you see only empty left side with ./ and ../ only.
I don't know if it's Java, Ubuntu or Spine issue.