Recently upgraded from CLM 5.0.2 to 6.0.1 and SystemErr.log has:
java.util.zip.ZipException: Exception in opening zip file: /data/apps/WAS8/AppServer/profiles/rwppad/temp/sdwbrat2Node11/rwppad/pad-jazz/jazz.war/eclipse/configuration/org.eclipse.osgi/bundles/512/1/bundlefile
        at org.eclipse.osgi.framework.util.SecureAction.getZipFile(SecureAction.java:264)
        at org.eclipse.osgi.baseadaptor.bundlefile.ZipBundleFile.basicOpen(ZipBundleFile.java:88)
        at org.eclipse.osgi.baseadaptor.bundlefile.ZipBundleFile.getZipFile(ZipBundleFile.java:101)
        at org.eclipse.osgi.baseadaptor.bundlefile.ZipBundleFile.checkedOpen(ZipBundleFile.java:74)
        at org.eclipse.osgi.baseadaptor.bundlefile.ZipBundleFile.getEntry(ZipBundleFile.java:246)
        at org.eclipse.equinox.weaving.hooks.WeavingBundleFile.getEntry(Unknown Source)
        at org.eclipse.osgi.baseadaptor.bundlefile.BundleFileWrapperChain.getEntry(BundleFileWrapperChain.java:44)
        at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findClassImpl(ClasspathManager.java:531)
        at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClassImpl(ClasspathManager.java:481)
        at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClass_LockClassName(ClasspathManager.java:460)
        at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClass(ClasspathManager.java:447)
        at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.findLocalClass(DefaultClassLoader.java:216)
        at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:393)
        at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:469)
        at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:422)
        at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:410)
        at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:663)
        at com.ibm.team.build.internal.service.notification.BuildNotifier.run(BuildNotifier.java:331)
        at com.ibm.team.build.internal.service.notification.BuildNotificationTask.runTask(BuildNotificationTask.java:39)
        at com.ibm.team.repository.service.async.AbstractAutoScheduledTask.executeTask(AbstractAutoScheduledTask.java:96)
        at sun.reflect.GeneratedMethodAccessor229.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
        at java.lang.reflect.Method.invoke(Method.java:611)
        at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord.invoke(ExportProxyServiceRecord.java:361)
        at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord.access$0(ExportProxyServiceRecord.java:347)
        at org.eclipse.soda.sat.core.internal.record.ExportProxyServiceRecord$ExportedServiceInvocationHandler.invoke(ExportProxyServiceRecord.java:56)
        at com.sun.proxy.$Proxy1407.executeTask(Unknown Source)
        at com.ibm.team.repository.service.internal.scheduler.AsynchronousTaskRunner.runTask(AsynchronousTaskRunner.java:185)
        at com.ibm.team.repository.service.internal.scheduler.AsynchronousTaskRunner.run(AsynchronousTaskRunner.java:138)
        at java.lang.Thread.run(Thread.java:790)
Caused by: java.util.zip.ZipException: error in opening zip file
        at java.util.zip.ZipFile.open(Native Method)
        at java.util.zip.ZipFile.<init>(ZipFile.java:140)
        at java.util.zip.ZipFile.<init>(ZipFile.java:157)
        at org.eclipse.osgi.framework.util.SecureAction.getZipFile(SecureAction.java:251)
        ... 30 more

ls -l /data/apps/WAS8/AppServer/profiles/rwppad/temp/sdwbrat2Node11/rwppad/pad-jazz/jazz.war/eclipse/configuration/org.eclipse.osgi/bundles/512/1/bundlefile
-rw-r--r--    1 rwppad   rwppad        29325 Apr 22 20:41 /data/apps/WAS8/AppServer/profiles/rwppad/temp/sdwbrat2Node11/rwppad/pad-jazz/jazz.war/eclipse/configuration/org.eclipse.osgi/bundles/512/1/bundlefile

file /data/apps/WAS8/AppServer/profiles/rwppad/temp/sdwbrat2Node11/rwppad/pad-jazz/jazz.war/eclipse/configuration/org.eclipse.osgi/bundles/512/1/bundlefile
/data/apps/WAS8/AppServer/profiles/rwppad/temp/sdwbrat2Node11/rwppad/pad-jazz/jazz.war/eclipse/configuration/org.eclipse.osgi/bundles/512/1/bundlefile: PKZIP (.zip) compressed archive

sum /data/apps/WAS8/AppServer/profiles/rwppad/temp/sdwbrat2Node11/rwppad/pad-rm/rm.war/eclipse/configuration/org.eclipse.osgi/bundles/401/1/bundlefile
47778    29 /data/apps/WAS8/AppServer/profiles/rwppad/temp/sdwbrat2Node11/rwppad/pad-jazz/jazz.war/eclipse/configuration/org.eclipse.osgi/bundles/512/1/bundlefile

/usr/java6/bin/jar -xvf /data/apps/WAS8/AppServer/profiles/rwppad/temp/sdwbrat2Node11/rwppad/pad-jazz/jazz.war/eclipse/configuration/org.eclipse.osgi/bundles/512/1/bundlefile
  created: META-INF/
 inflated: META-INF/MANIFEST.MF
  created: com/
  created: com/ibm/
  created: com/ibm/team/
  created: com/ibm/team/build/
  created: com/ibm/team/build/internal/
  created: com/ibm/team/build/internal/service/
  created: com/ibm/team/build/internal/service/notification/
  created: resources/
  created: resources/process/
  created: schema/
 inflated: com/ibm/team/build/internal/service/notification/BuildNotificationTask.class
 inflated: com/ibm/team/build/internal/service/notification/BuildNotifier$1.class
 inflated: com/ibm/team/build/internal/service/notification/BuildNotifier.class
 inflated: com/ibm/team/build/internal/service/notification/Messages.class
 inflated: com/ibm/team/build/internal/service/notification/messages.properties
 inflated: plugin.properties
 inflated: plugin.xml
 inflated: resources/process/category-description.html
 inflated: schema/notification.xsd