I've got a Arquillian (1.0.0.alpha-3) IN_CONTAINER test running against JBoss AS 6 (trunk) remote. The test is simple - it just deploys a WebArchive and does a lookup of a EJB that's deployed in the .war (AS6 supports EJB deployments in .war):

@RunWith(Arquillian.class)
@Run(RunModeType.IN_CONTAINER)
public class JNDIAccessTestCase
{

   private static final String MODULE_NAME = "hello";
   
   
   @Deployment
   public static WebArchive createDeployment() throws Exception
   {
      return ShrinkWrap.create(WebArchive.class, MODULE_NAME + ".war").addPackage(JNDIAccessTestCase.class.getPackage());
   }
   
   @Test
   public void testSimpleJNDIAccess() throws Exception
   {
      Context ctx = new InitialContext();
      Echo bean = (Echo) ctx.lookup("blah");
      String echo = bean.echo("msg");
   }
}

As you can see, I just deploy the hello.war. While running this test, I keep running into the following exception and Arquillian fails to fire the testcase:

Caused by: java.lang.IllegalStateException: Error launching test org.jboss.bean.integration.test.jndi.JNDIAccessTestCase public void org.jboss.bean.integration.test.jndi.JNDIAccessTestCase.testSimpleJNDIAccess() throws java.lang.Exception
    at org.jboss.arquillian.protocol.servlet_3.ServletMethodExecutor.invoke(ServletMethodExecutor.java:61)
    at org.jboss.arquillian.impl.handler.ContainerTestExecuter.callback(ContainerTestExecuter.java:50)
    at org.jboss.arquillian.impl.handler.ContainerTestExecuter.callback(ContainerTestExecuter.java:40)
    at org.jboss.arquillian.impl.event.MapEventManager.fire(MapEventManager.java:63)
    ... 26 more
Caused by: java.lang.IllegalStateException: Error launching test at http://localhost:8080/test/ArquillianServletRunner?outputMode=serializedObject&className=org.jboss.bean.integration.test.jndi.JNDIAccessTestCase&methodName=testSimpleJNDIAccess. Kept on getting 404s.
    at org.jboss.arquillian.protocol.servlet_3.ServletMethodExecutor.execute(ServletMethodExecutor.java:125)
    at org.jboss.arquillian.protocol.servlet_3.ServletMethodExecutor.invoke(ServletMethodExecutor.java:57)
    ... 29 more
    

So it appears that Arquillian deploys the hello.war (at hello context) and then tries to run the in-container test by using the hardcoded "test" context. This is what I see in org.jboss.arquillian.protocol.servlet_3.ServletMethodExecutor.invoke:

public TestResult invoke(TestMethodExecutor testMethodExecutor) 
   {
      if(testMethodExecutor == null) 
      {
         throw new IllegalArgumentException("TestMethodExecutor must be specified");
      }
      
      Class<?> testClass = testMethodExecutor.getInstance().getClass();
      String url = baseURL.toExternalForm() + "test/ArquillianServletRunner" +  
                        "?outputMode=serializedObject&className=" + testClass.getName() + 
                        "&methodName=" + testMethodExecutor.getMethod().getName();
      
      try 
      {
         return execute(url);
      } 
      catch (Exception e) 
      {
         throw new IllegalStateException("Error launching test " + testClass.getName() + " " + testMethodExecutor.getMethod(), e);
      }
   }