Application hang ? Perhaps white one of the threads is blocked on system.in

Hi All,
I have a SE application that does mainly GUI and takes additional input from System.in.
It seems that the application hangs from time to time.
Weired enough, my way to reproduce the problem is by running MS Spy++ while the application is waiting for input from System.in
I'm in the dark - any clues?
Thanks,
Jacky

First, thanks for your quick reply. Here are some more details (which I probably should included in the first place)
My code has two threads - The main that does the GUI (Swing).
The second thread takes input from external process (as a pipe) using:
private Scanner scanner = new Scanner(new BufferedInputStream( System.in), "UTF-8");
and:
String s = scanner.next();
I tried to use system.in.available() and scanner.hasNext() to make sure that I have something to read but it didn't seem to help.
One more data point - the problem seems to happen in Windows XP but not with Win 7.
Thanks for the help,
Jacky

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Application hang ? Perhaps white one of the threads is blocked on system.in

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