I really don't know how bad this is or the real source of the problem, but I started IGB without clearing everything first, with it set to Arabidopsis (1 track). when it started up, I got this sequence of errors (I have seen this before - but not consistently...). I am reporting this for you to look at - if you can't reproduce it or it isn't actually an issue, feel free to kill this bug, but just in case it IS real...

loading default prefs from: /igb_default_prefs.xml
loading user prefs from: http://eos.transvar.org:8080/igb_release//igb_prefs.xml
loading prefs from url: http://eos.transvar.org:8080/igb_release//igb_prefs.xml
DAS server version: , status:
DAS capabilities:
Initializing http://bioviz.org/das2/genome
MainWorkspaceManager:itemStateChanged hit
MainWorkspaceManager:itemStateChanged hit
MainWorkspaceManager:itemStateChanged hit
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.view.load.DataManagementTableModel.clearFeatures(DataManagementTableModel.java:78)
at com.affymetrix.igb.view.load.GeneralLoadView.refreshTree(GeneralLoadView.java:402)
at com.affymetrix.igb.view.load.GeneralLoadView.access$100(GeneralLoadView.java:60)
at com.affymetrix.igb.view.load.GeneralLoadView$3.run(GeneralLoadView.java:394)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
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)
MainWorkspaceManager:itemStateChanged hit
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.view.load.DataManagementTableModel.clearFeatures(DataManagementTableModel.java:78)
at com.affymetrix.igb.view.load.GeneralLoadView.refreshTree(GeneralLoadView.java:402)
at com.affymetrix.igb.view.load.GeneralLoadView.access$100(GeneralLoadView.java:60)
at com.affymetrix.igb.view.load.GeneralLoadView$3.run(GeneralLoadView.java:394)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
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)
WARNING: Could not find Das2 server http://netaffxdas.affymetrix.com/das2/genome
WARNING: Couldn't find species for server: NetAffx

-------------------------------------------------------
NetAffx: Server NetAffx is not responding. Disabling it for this session.
-------------------------------------------------------

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.view.load.DataManagementTableModel.clearFeatures(DataManagementTableModel.java:78)
at com.affymetrix.igb.view.load.GeneralLoadView.refreshTree(GeneralLoadView.java:402)
at com.affymetrix.igb.view.load.GeneralLoadView.access$100(GeneralLoadView.java:60)
at com.affymetrix.igb.view.load.GeneralLoadView$3.run(GeneralLoadView.java:394)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:205)
at java.awt.Dialog$1.run(Dialog.java:1046)
at java.awt.Dialog$3.run(Dialog.java:1098)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Dialog.show(Dialog.java:1096)
at java.awt.Component.show(Component.java:1584)
at java.awt.Component.setVisible(Component.java:1536)
at java.awt.Window.setVisible(Window.java:842)
at java.awt.Dialog.setVisible(Dialog.java:986)
at com.affymetrix.genometryImpl.util.ErrorHandler.processDialog(ErrorHandler.java:78)
at com.affymetrix.genometryImpl.util.ErrorHandler.access$000(ErrorHandler.java:33)
at com.affymetrix.genometryImpl.util.ErrorHandler$1.run(ErrorHandler.java:164)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
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)
MainWorkspaceManager:itemStateChanged hit
BED annot count: 9263
BED annot count: 5558
BED annot count: 6907
BED annot count: 5355
BED annot count: 8088
BED annot count: 88
BED annot count: 122