In my experience if you do not apply look-and-feel separately to JFileChooser, you see initial LF. So i think you can apply a different LF to your JFileChooser. An example code is in the url below if you need (you need to call SwingUtilities.updateComponentTreeUI(..) only on JFileChooser):
How to change the look and feel of Swing applications
http://www.java-tips.org/content/view/762/2/