I have tried the same 'ls' scenario to open a shell about 30 times but could not reproduce the problem.

OK, I just ran into this problem:

java.lang.ArrayIndexOutOfBoundsException
    at java.lang.System.arraycopy(Native Method)
    at org.netbeans.lib.terminalemulator.Line.getChars(Line.java:195)
    at org.netbeans.lib.terminalemulator.Term.paint_line_new(Term.java:3084)
    at org.netbeans.lib.terminalemulator.Term.do_paint(Term.java:3365)
    at org.netbeans.lib.terminalemulator.Screen.paint(Screen.java:199)
    at javax.swing.JComponent.paintChildren(JComponent.java:862)
    at javax.swing.JComponent.paint(JComponent.java:1038)
    at javax.swing.JComponent.paintChildren(JComponent.java:862)
    at javax.swing.JComponent.paint(JComponent.java:1038)
    at javax.swing.JComponent.paintToOffscreen(JComponent.java:5124)
    at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:278)
    at javax.swing.RepaintManager.paint(RepaintManager.java:1225)
    at javax.swing.JComponent._paintImmediately(JComponent.java:5072)
    at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
    at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:786)
    at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:714)
    at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:694)
    at javax.swing.RepaintManager.access$700(RepaintManager.java:41)
    at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1636)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:646)
    at java.awt.EventQueue.access$000(EventQueue.java:84)
    at java.awt.EventQueue$1.run(EventQueue.java:607)
    at java.awt.EventQueue$1.run(EventQueue.java:605)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:616)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
 

I could not reproduce this problem consistently. In fact, I have only run into this problem once since you logged this issue.

Tried to reproduce this issue several times on Ubuntu 12.04 using ADStudio 12 Dev 23, however with no success, the issue did not occurred.

Another test case for this problem is described in issue 6948:
  https://www.aquaclusters.com/app/home/project/public/aquadatastudio/issue/6948
I could not reproduce 6948 in my environment either, though.

I have been using the 'ls' scenario to open a shell in my environment since 5/12, no luck. I also tried SQL described in issue 6948 once every couple of days, could not reproduce the problem either.

This problem is triggered from the Swing EDT and happened in the low level Term object, it is not possible to figure out what has gone wrong if we cannot consistently reproduce this problem.

Does not occur with newer builds - 12.0.0-dev-31