JFileChooser is unlike native windows in Handling stale shortcuts. 

Steps to reproduce:
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1) Make a tmp dir and make a shortcut of it on Desktop. You can right click on the newly dir and click sentto Desktop as shortcut. 
2) Now Delete the Dir. Do NOT delete the short cut. 
3) Now Open SwingSet2 on b50. 
4) Goto FileChooser Demo. 
5) Click on show plain FileChooser. 
6) You will see a dialog stating with title "Problem with ShortCut". This Dialog will appear two times.
&) Now Open WordPad. Open Native Filechooser by Prerssing ctrl+O
7) Navigate to Desktop from the filechooser and notice that there is no dialog. 
8) Now go back to FileChooser Demo and navigate to desktop. as soon as you click  Desktop in Look in combo you will see the same Dialog. This time it comes for six times. 
9) Also if you go to any other folder like My Computer or C:/ or a map drive you will see this dialog. 

This nehavior is not shown till b49. For Error dilaog see the image attached.