Load 2 graphs, join. Make sure they are NOT collapsed (each individual graph has it's 'thumb' exposed). Using the 'thumb', select one graph and use the 'Delete Graph' button in the Graph tab. Delete the second in the same way. Deleting the tracks in the joined track should just delete the joined track as well as the track. The error trace is as follows:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.trackAdjuster.TrackPreferencesSeqMapViewPanel.refreshSelection(TrackPreferencesSeqMapViewPanel.java:38)
at com.affymetrix.igb.trackAdjuster.TrackPreferencesSeqMapViewPanel.trackstylePropertyChanged(TrackPreferencesSeqMapViewPanel.java:90)
at com.affymetrix.igb.shared.TrackstylePropertyMonitor.firePropertyChanged(TrackstylePropertyMonitor.java:47)
at com.affymetrix.igb.shared.TrackstylePropertyMonitor.tableChanged(TrackstylePropertyMonitor.java:29)
at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:280)
at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:182)
at com.affymetrix.igb.view.load.DataManagementTableModel.setValueAt(DataManagementTableModel.java:322)
at javax.swing.JTable.setValueAt(JTable.java:2710)
at com.jidesoft.grid.JideTable.editingStopped(Unknown Source)
at javax.swing.AbstractCellEditor.fireEditingStopped(AbstractCellEditor.java:125)
at com.affymetrix.genoviz.swing.ButtonTableCellEditor.actionPerformed(ButtonTableCellEditor.java:61)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.Component.processMouseEvent(Component.java:6375)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6140)
at java.awt.Container.processEvent(Container.java:2083)
at java.awt.Component.dispatchEventImpl(Component.java:4737)
at java.awt.Container.dispatchEventImpl(Container.java:2141)
at java.awt.Component.dispatchEvent(Component.java:4565)
at javax.swing.plaf.basic.BasicTableUI$Handler.repostEvent(BasicTableUI.java:918)
at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1134)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:273)
at java.awt.Component.processMouseEvent(Component.java:6375)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6140)
at java.awt.Container.processEvent(Container.java:2083)
at java.awt.Component.dispatchEventImpl(Component.java:4737)
at java.awt.Container.dispatchEventImpl(Container.java:2141)
at java.awt.Component.dispatchEvent(Component.java:4565)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4280)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)
at java.awt.Container.dispatchEventImpl(Container.java:2127)
at java.awt.Window.dispatchEventImpl(Window.java:2482)
at java.awt.Component.dispatchEvent(Component.java:4565)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:684)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:643)
at java.awt.EventQueue$1.run(EventQueue.java:641)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
at java.awt.EventQueue$2.run(EventQueue.java:657)
at java.awt.EventQueue$2.run(EventQueue.java:655)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:654)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.trackAdjuster.TrackPreferencesSeqMapViewPanel.refreshSelection(TrackPreferencesSeqMapViewPanel.java:38)
at com.affymetrix.igb.trackAdjuster.TrackPreferencesSeqMapViewPanel.trackstylePropertyChanged(TrackPreferencesSeqMapViewPanel.java:90)
at com.affymetrix.igb.shared.TrackstylePropertyMonitor.firePropertyChanged(TrackstylePropertyMonitor.java:47)
at com.affymetrix.igb.shared.TrackstylePropertyMonitor.tableChanged(TrackstylePropertyMonitor.java:29)
at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:280)
at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:182)
at com.affymetrix.igb.view.load.DataManagementTableModel.createVirtualFeatures(DataManagementTableModel.java:91)
at com.affymetrix.igb.view.load.GeneralLoadView$5.run(GeneralLoadView.java:427)
at com.affymetrix.genometryImpl.util.ThreadUtils.runOnEventQueue(ThreadUtils.java:29)
at com.affymetrix.igb.view.load.GeneralLoadView.refreshDataManagementTable(GeneralLoadView.java:423)
at com.affymetrix.igb.view.load.GeneralLoadView.refreshDataManagementView(GeneralLoadView.java:435)
at com.affymetrix.igb.view.load.GeneralLoadView$8.finished(GeneralLoadView.java:653)
at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:54)
at javax.swing.SwingWorker$5.run(SwingWorker.java:717)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814)
at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824)
at javax.swing.Timer.fireActionPerformed(Timer.java:291)
at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:643)
at java.awt.EventQueue$1.run(EventQueue.java:641)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:652)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)