We tried to extract all the records from a couple of ns5 document using the notes 8 api. Notes crashes consistently with the following error message. However we found that the crash does not happen if the files were extracted using the 6.5 api. nfixup does not detect any errors as well.
trace-log-0.xml
Time Severity Message Subsystem Source Class.Method Thread Id
2008-12-30T11:09:48.655-08:00 CONFIG eclipse.buildId=build20070731-1521
java.fullversion=J2RE 1.5.0 IBM J9 2.3 Windows Server 2003 x86-32 j9vmwi3223ifx-20070714 (JIT enabled)
J9VM - 20070713_13151_lHdSMR
JIT - 20070109_1805ifx5_r8
GC - 200701_09
BootLoader constants: OS=win32
, ARCH=x86
, WS=win32
, NL=en_US
Framework arguments: -dir ltr -personality com.ibm.rcp.platform.personality -product com.ibm.notes.branding.notes -plugincustomization C:/Program Files/IBM/Lotus/Notes/framework/rcp/plugin_customization.ini
Command-line arguments: -os win32 -ws win32 -arch x86 -dir ltr -personality com.ibm.rcp.platform.personality -product com.ibm.notes.branding.notes -data C:\Program Files\IBM\Lotus\Notes\Data\workspace -plugincustomization C:/Program Files/IBM/Lotus/Notes/framework/rcp/plugin_customization.ini
com.ibm.rcp.core.internal.logger.frameworkhook com.ibm.rcp.core.internal.logger.frameworkhook .writeSession 10
2008-12-30T11:10:15.139-08:00 INFO [Fatal Error] 
-1: Premature end of file.
SystemErr 13
2008-12-30T11:10:51.764-08:00 SEVERE Widget disposed too early!
java.lang.RuntimeException: Widget disposed too early!
at org.eclipse.ui.internal.WorkbenchPartReference$1.widgetDisposed(WorkbenchPartReference.java:153)
at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:116)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:66)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:938)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:962)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:943)
at org.eclipse.swt.widgets.Widget.release(Widget.java:740)
at org.eclipse.swt.widgets.Composite.releaseChildren(Composite.java:662)
at org.eclipse.swt.widgets.Widget.release(Widget.java:743)
at org.eclipse.swt.widgets.Composite.releaseChildren(Composite.java:662)
at org.eclipse.swt.widgets.Widget.release(Widget.java:743)
at org.eclipse.swt.widgets.Composite.releaseChildren(Composite.java:662)
at org.eclipse.swt.widgets.Widget.release(Widget.java:743)
at org.eclipse.swt.widgets.Composite.releaseChildren(Composite.java:662)
at org.eclipse.swt.widgets.Widget.release(Widget.java:743)
at org.eclipse.swt.widgets.Composite.releaseChildren(Composite.java:662)
at org.eclipse.swt.widgets.Canvas.releaseChildren(Canvas.java:117)
at org.eclipse.swt.widgets.Decorations.releaseChildren(Decorations.java:782)
at org.eclipse.swt.widgets.Shell.releaseChildren(Shell.java:1134)
at org.eclipse.swt.widgets.Widget.release(Widget.java:743)
at org.eclipse.swt.widgets.Widget.dispose(Widget.java:410)
at org.eclipse.swt.widgets.Decorations.dispose(Decorations.java:457)
at org.eclipse.swt.widgets.Shell.dispose(Shell.java:653)
at org.eclipse.jface.window.Window.close(Window.java:330)
at org.eclipse.jface.window.ApplicationWindow.close(ApplicationWindow.java:299)
at org.eclipse.ui.internal.WorkbenchWindow.hardClose(WorkbenchWindow.java:1549)
at org.eclipse.ui.internal.WorkbenchWindow.busyClose(WorkbenchWindow.java:625)
at org.eclipse.ui.internal.WorkbenchWindow.access$1(WorkbenchWindow.java:601)
at org.eclipse.ui.internal.WorkbenchWindow$2.run(WorkbenchWindow.java:716)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:67)
at org.eclipse.ui.internal.WorkbenchWindow.close(WorkbenchWindow.java:714)
at org.eclipse.jface.window.WindowManager.close(WindowManager.java:109)
at org.eclipse.ui.internal.Workbench$12.run(Workbench.java:716)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:37)
at org.eclipse.ui.internal.Workbench.busyClose(Workbench.java:713)
at org.eclipse.ui.internal.Workbench.access$8(Workbench.java:643)
at org.eclipse.ui.internal.Workbench$15.run(Workbench.java:856)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:67)
at org.eclipse.ui.internal.Workbench.close(Workbench.java:854)
at org.eclipse.ui.internal.Workbench.close(Workbench.java:829)
at org.eclipse.ui.internal.WorkbenchWindow.busyClose(WorkbenchWindow.java:622)
at org.eclipse.ui.internal.WorkbenchWindow.access$1(WorkbenchWindow.java:601)
at org.eclipse.ui.internal.WorkbenchWindow$2.run(WorkbenchWindow.java:716)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:67)
at org.eclipse.ui.internal.WorkbenchWindow.close(WorkbenchWindow.java:714)
at org.eclipse.jface.window.Window.handleShellCloseEvent(Window.java:736)
at org.eclipse.jface.window.Window$3.shellClosed(Window.java:682)
at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:91)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:66)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:938)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:962)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:947)
at org.eclipse.swt.widgets.Decorations.closeWidget(Decorations.java:301)
at org.eclipse.swt.widgets.Shell.close(Shell.java:476)
at com.ibm.workplace.noteswc.listeners.PlatformShutdownListener$2.runInUIThread(PlatformShutdownListener.java:301)
at org.eclipse.ui.progress.UIJob$1.run(UIJob.java:94)
at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35)
at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:123)
at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:3659)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3296)
at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:1931)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:1895)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:423)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
at com.ibm.rcp.personality.framework.internal.RCPApplication.run(RCPApplication.java:72)
at org.eclipse.core.internal.runtime.PlatformActivator$1.run(PlatformActivator.java:78)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:92)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:68)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:400)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:177)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:64)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:615)
at org.eclipse.core.launcher.Main.invokeFramework(Main.java:336)
at org.eclipse.core.launcher.Main.basicRun(Main.java:280)
at org.eclipse.core.launcher.Main.run(Main.java:977)
at com.ibm.rcp.core.internal.launcher.Main.startLaunch(Main.java:895)
at com.ibm.rcp.core.internal.launcher.Main.main(Main.java:1313)
org.eclipse.ui.workbench 11
Time Severity Message Subsystem
2008-12-22T14:59:30.470-08:00 SEVERE CLFNM0237E: The CSIDelgateUtil failed to open a runtime document from CSI com.ibm.rcp.csiviews.util.CSIDelegateUtil
2008-12-22T14:59:30.470-08:00 SEVERE Argument cannot be null com.ibm.rcp.csiviews.viewpart.CSIViewPart