Interesting problem.

Here's the contents of my jndi.properties (which is likely the first time I've looked at this file):

# DO NOT EDIT THIS FILE UNLESS YOU KNOW WHAT YOU ARE DOING
#
java.naming.factory.initial=org.jboss.naming.JBossRemotingContextFactory
java.naming.factory.url.pkgs=org.jboss.naming:org.jnp.interfaces

Have you tried installing the JDK 1.6 and JBoss AS on Windows or Linux to see if you can reproduce the problem?

Have a look at this class: org.jboss.seam.init.Initialization

public Initialization create()
   {
      standardDeploymentStrategy = new StandardDeploymentStrategy(Thread.currentThread().getContextClassLoader());
      standardDeploymentStrategy.scan();
      addNamespaces();
      initComponentsFromXmlDocument("/WEB-INF/components.xml");
      initComponentsFromXmlDocument("/WEB-INF/events.xml"); //deprecated
      initComponentsFromXmlDocuments();
      initPropertiesFromServletContext();
      initPropertiesFromResource();
      initJndiProperties();
      initPropertiesFromSystem();
      return this;
   }

private void initJndiProperties()
   {
      Properties jndiProperties = new Properties();
      jndiProperties.putAll(loadFromResource("/jndi.properties"));
      jndiProperties.putAll(loadFromResource("/seam-jndi.properties"));
      Naming.setInitialContextProperties(jndiProperties);
   }

   private Properties loadFromResource(String resource)
   {
      Properties props = new Properties();
      InputStream stream = Resources.getResourceAsStream(resource, servletContext);
      if (stream != null)
      {
         try
         {
            log.info("reading properties from: " + resource);
            try
            {
               props.load(stream);
            }
            catch (IOException ioe)
            {
               log.error("could not read " + resource, ioe);
            }
         }
         finally 
         {
            Resources.closeStream(stream);
         }
      }
      else
      {
         log.debug("not found: " + resource);
      }
      return props;
   }

I do not see a jndi.properties in this location:

C:\java\jboss-5.1.0.GA\server\default\deployers\jbossweb.deployer

Is it possible that Seam/Jboss is not finding that file??

If you can't reproduce in Windows environment with same build, JDK and JBoss, then it seems like a bug to me or a configuration issue.

If you purchase a JBoss developer subscription for EAP then you could open a case with the support techs to trouble-shoot this...  $3500 per person, unlimited incidents.