The problem that Im seeing maybe related to issue 22561 in 
which the user had difficulty executing a JSP on a fat32 
based system.  Im having a similar problem executing a 
plain servlet.  The execution that i recieve is 
different.  The specific builds that I have tried are from 
20020528,0529,0530,0531.
I have used the 3.3.1 release version on fat32 and the web 
module works fine there.
I have been able to recreate this on 3 different machines 
all running xp.  One of them is also a dualboot win98se 
machine.  I get the same result in win98.
These are the steps that i follow:
unzip netbeans & run netbeans (making sure that there is 
no previous configuration by deleting .netbeans in the 
home directory)
unmount the sample dir
Create a new web-module in another location.
Create a new servlet (using menu->wizard).
Execute the servlet and get the following exception:
Annotation: Exception occurred in Request Processor

java.lang.NullPointerException
        at 
org.apache.xerces.dom.NamedNodeMapImpl.findNamePoint
(NamedNodeMapImpl.java:476)
        at 
org.apache.xerces.dom.NamedNodeMapImpl.getNamedItem
(NamedNodeMapImpl.java:169)
        at org.apache.xerces.dom.ElementImpl.getAttribute
(ElementImpl.java:219)
        at 
org.netbeans.modules.web.xmlutils.XMLJ2eeUtils.addElement
(XMLJ2eeUtils.java:483)
        at 
org.netbeans.modules.tomcat.tomcat40.Tomcat40DataObject.add
ContextLogger(Tomcat40DataObject.java:1151)
        at 
org.netbeans.modules.tomcat.tomcat40.Tomcat40DataObject.set
NewContext(Tomcat40DataObject.java:612)
        at 
org.netbeans.modules.tomcat.tomcat40.Tomcat40Installation.s
etTestComponent(Tomcat40Installation.java:616)
        at 
org.netbeans.modules.tomcat.tomcat40.Tomcat40Installation.i
ncrementalDeploy(Tomcat40Installation.java:603)
        at 
org.netbeans.modules.tomcat.tomcat40.Tomcat40Instance.deplo
y(Tomcat40Instance.java:260)
        at 
org.netbeans.modules.j2ee.impl.DefaultServerInstanceManager
.doDeploy(DefaultServerInstanceManager.java:136)
        at 
org.netbeans.modules.j2ee.impl.DefaultServerInstanceManager
.startExecution(DefaultServerInstanceManager.java:150)
        at 
org.netbeans.modules.j2ee.impl.DefaultServerInstanceManager
.serverInstanceStartExecution
(DefaultServerInstanceManager.java:101)
        at 
org.netbeans.modules.j2ee.impl.DefaultExecPerformer.startEx
ecution(DefaultExecPerformer.java:105)
        at 
org.netbeans.modules.web.execution.WebDefaultExecPerformer.
startExecution(WebDefaultExecPerformer.java:246)
        at 
org.netbeans.modules.j2ee.impl.ServerExecutor.execute
(ServerExecutor.java:74)
        at 
org.netbeans.modules.j2ee.impl.ServerExecutor.execute
(ServerExecutor.java:64)
        at org.openide.loaders.ExecSupport.start
(ExecSupport.java:103)
        at org.openide.actions.ExecuteAction.execute
(ExecuteAction.java:139)
        at org.openide.actions.ExecuteAction.execute
(ExecuteAction.java:236)
        at org.openide.actions.ExecuteAction.performAction
(ExecuteAction.java:101)
        at 
org.openide.util.actions.NodeAction.performAction
(NodeAction.java:179)
        at 
org.openide.util.actions.NodeAction.actionPerformed
(NodeAction.java:170)
        at org.netbeans.core.ModuleActions$1.run
(ModuleActions.java:100)
        at org.openide.util.Task.run(Task.java:136)
[catch] at org.openide.util.RequestProcessor$Processor.run
(RequestProcessor.java:599)

The tomcat instance does not start and the servlet does 
not run, serlvet.xml file is not modified.  Web.xml file 
within the web-module, WEB-INF directory is modified to 
include the servlet link.

I also needed to modify the tomcat port on one of the 
machines and the server.xml file was wiped out:  
After changing the port attribute under runtime,server 
registry,installed servers, tomcat 4.0,internal,localhost 
the following is
written to the server.xml file

<!-- Basic Server configuration file for Netbeans/FFJ -->
[Server: null]


I have done all of these steps on the release version and 
they work fine.  I have done all of these steps with the 
0531 version on an ntfs file system on one of these 
computers and it works fine as well.

If I can provide further details, please let me know.