ClearCase is an experimental profile for NetBeans and we can not test it.

From that report I do not see what's the real problem. You said, that the JSE 
project was created, but broken. Does that mean that there is problem in
creation of only some specific files? Are the directories read-only? Can you
create the files in shell?

Can that be caused by channel.tryLock()? Perhaps it does something that NFS+VOB
does not like...

Situation with file system and broken project is the following:

VOB directory is checked out.
We can create view private files and directories from shell.
We can create CC controlled directories and files using 'cleartool'.

After failed attempt to create project in registered VOB directory, we have the
following directories and files structure:

VOB directory is: '/export/ClearCase/testccvob'

bash-2.05$ pwd
/export/ClearCase/testccvob
bash-2.05$ ls -al
total 7
drwxr-xr-x   6 avk      java         217 Jan 16 21:57 .
drwxrwxr-x   8 root     orion        512 Jan  7 15:15 ..
-rw-r--r--   1 avk      java         708 Jan 15 23:26 .nbintdb
drwxr-xr-x   5 avk      java         286 Jan 15 20:59 AnagramGame
drwxr-xr-x   3 avk      java         141 Jan 16 21:57 JavaApplication4
drwxr-xr-x   2 avk      java           0 Jan  7 15:13 lost+found
drwxr-xr-x   2 avk      java           0 Jan 16 21:46 vvv
bash-2.05$ ls -al JavaApplication4/
total 3
drwxr-xr-x   3 avk      java         141 Jan 16 21:57 .
drwxr-xr-x   6 avk      java         217 Jan 16 21:57 ..
drwxr-xr-x   2 avk      java         202 Jan 16 21:57 nbproject
bash-2.05$ ls -al JavaApplication4/nbproject/
total 2
drwxr-xr-x   2 avk      java         202 Jan 16 21:57 .
drwxr-xr-x   3 avk      java         141 Jan 16 21:57 ..
-rw-r--r--   1 avk      java           0 Jan 16 21:57 .LCKproject.xml~
-rw-r--r--   1 avk      java           0 Jan 16 21:57 project.xml



About channel.tryLock() as a cause of a problem:
The following exception is thrown in console (paste it because you have no
ability to reproduce this bug):

bash-2.05$ INFORMATIONAL *********** Exception occurred ************ at 10:13 PM
on Jan 16, 2005
Annotation: Invalid argument
java.io.IOException: Invalid argument
        at sun.nio.ch.FileChannelImpl.lock0(Native Method)
        at sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:822)
        at java.nio.channels.FileChannel.tryLock(FileChannel.java:967)
        at
org.netbeans.modules.masterfs.filebasedfs.fileobjects.WriteLock.<init>(WriteLock.java:85)
        at
org.netbeans.modules.masterfs.filebasedfs.fileobjects.WriteLock.tryLock(WriteLock.java:64)
        at
org.netbeans.modules.masterfs.Delegate$FileLockImpl.initLock(Delegate.java:260)
        at
org.netbeans.modules.masterfs.Delegate$FileLockImpl.access$200(Delegate.java:243)
        at org.netbeans.modules.masterfs.Delegate.lock(Delegate.java:170)
        at
org.netbeans.modules.masterfs.MasterFileObject.lock(MasterFileObject.java:154)
        at
org.netbeans.spi.project.support.ant.ProjectGenerator$1.run(ProjectGenerator.java:99)
        at org.openide.util.Mutex.writeAccess(Mutex.java:310)
        at
org.netbeans.spi.project.support.ant.ProjectGenerator.createProject0(ProjectGenerator.java:78)
        at
org.netbeans.spi.project.support.ant.ProjectGenerator.createProject(ProjectGenerator.java:73)
        at
org.netbeans.modules.java.j2seproject.J2SEProjectGenerator.createProject(J2SEProjectGenerator.java:138)
        at
org.netbeans.modules.java.j2seproject.J2SEProjectGenerator.createProject(J2SEProjectGenerator.java:58)
        at
org.netbeans.modules.java.j2seproject.ui.wizards.NewJ2SEProjectWizardIterator.instantiate(NewJ2SEProjectWizardIterator.java:118
        at
org.openide.loaders.TemplateWizard$Brigde2Iterator.instantiate(TemplateWizard.java:969)
        at
org.openide.loaders.TemplateWizard.handleInstantiate(TemplateWizard.java:557)
        at
org.openide.loaders.TemplateWizard.instantiateNewObjects(TemplateWizard.java:396)
        at
org.openide.loaders.TemplateWizardIterImpl.instantiate(TemplateWizardIterImpl.java:218)
        at org.openide.WizardDescriptor.callInstantiate(WizardDescriptor.java:1425)
        at org.openide.WizardDescriptor.access$900(WizardDescriptor.java:63)
[catch] at
org.openide.WizardDescriptor$Listener.actionPerformed(WizardDescriptor.java:1327)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
org.openide.util.WeakListenerImpl$ProxyListener.invoke(WeakListenerImpl.java:383)
        at $Proxy19.actionPerformed(Unknown Source)
        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)
        at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)
        at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
        at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:234)
        at java.awt.Component.processMouseEvent(Component.java:5488)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3093)
        at java.awt.Component.processEvent(Component.java:5253)
        at java.awt.Container.processEvent(Container.java:1966)
        at java.awt.Component.dispatchEventImpl(Component.java:3955)
        at java.awt.Container.dispatchEventImpl(Container.java:2024)
        at java.awt.Component.dispatchEvent(Component.java:3803)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)
        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)
        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
        at java.awt.Container.dispatchEventImpl(Container.java:2010)
        at java.awt.Window.dispatchEventImpl(Window.java:1766)
        at java.awt.Component.dispatchEvent(Component.java:3803)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
        at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:234)
        at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
        at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:153)
        at java.awt.Dialog$1.run(Dialog.java:515)
        at java.awt.Dialog.show(Dialog.java:536)
        at
org.netbeans.core.windows.services.NbPresenter.superShow(NbPresenter.java:800)
        at
org.netbeans.core.windows.services.NbPresenter.doShow(NbPresenter.java:843)
        at org.netbeans.core.windows.services.NbPresenter.run(NbPresenter.java:831)
        at org.openide.util.Mutex$1.run(Mutex.java:1058)
        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:199)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
        at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:234)
        at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

This seems related to http://www.netbeans.org/issues/show_bug.cgi?id=57534.
Though 57534 was reported against mac os x, it is in essence an issue reported
against file locking issues with NFS files.

The final comments from issue 57534:
   The issue remains in NetBeans 4.1 release. We have recommendation how to use
   this release and avoid the issue.
   The simple workaround is to copy module .jar file from NetBeans release 4.0
   (netbeans/platform4/modules/org-netbeans-modules-masterfs.jar)
   and paste it to release 4.1 build into the directory        
   netbeans/platform5/modules/
   Filelocking feature is missing then of course.
   I replaced the masterfs module and everythi ng works fine when working with
   project on remote server (accessed by samba). 

Possibly related:

http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6230772
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6174126

I've verified this bug using actual ClearCase VOB and VIEW with both versions of
masterfs.jar (from nb4.0 and nb4.1)

We have not this bug in nb4.0
We have bug in nb4.1 with native masterfs.jar
And this bug disappears if we start nb4.1 with masterfs.jar copied from nb4.0

About attempts to reproduce this bug: it is reproducible with actual ClearCase
VOB, but not with any directory mounted using NFS(it doesn't matter, if we
register directory mounted by nfs as a fake ClearCase VOB or simply create new
project in such directory).

Fixed by fixing Issue# 57534.