Arquillian Custom mode containers are not stopped on AfterSuite by default, their lifecyle is left completely up to the user/extensions. Example of a little extension that will stop the custom containers on AfterSuite.

CloseCustomContainersOnAfterSuiteExtension.java

/*
 * JBoss, Home of Professional Open Source
 * Copyright 2011 Red Hat Inc. and/or its affiliates and other contributors
 * as indicated by the @authors tag. All rights reserved.
 * See the copyright.txt in the distribution for a
 * full listing of individual contributors.
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * http://www.apache.org/licenses/LICENSE-2.0
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package my.testsuite;

import org.jboss.arquillian.container.spi.Container;
import org.jboss.arquillian.container.spi.Container.State;
import org.jboss.arquillian.container.spi.ContainerRegistry;
import org.jboss.arquillian.core.api.annotation.Observes;
import org.jboss.arquillian.core.spi.LoadableExtension;
import org.jboss.arquillian.test.spi.event.suite.AfterSuite;

/**
 * @author <a href="mailto:aslak@redhat.com">Aslak Knutsen</a>
 * @version $Revision: $
 */
public class CloseCustomContainersOnAfterSuiteExtension implements LoadableExtension
{
   @Override
   public void register(ExtensionBuilder builder)
   {
      builder.observer(CloseCustomContainers.class);
   }

   public static class CloseCustomContainers 
   {
      public void close(@Observes AfterSuite event, ContainerRegistry registry)
      {
         for(Container c : registry.getContainers())
         {
            if(c.getState() == State.STARTED && "custom".equalsIgnoreCase(c.getContainerConfiguration().getMode()))
            {
               try
               {
                  c.stop();
               }
               catch (Exception e) 
               {
                  System.err.println("Could not stop custom container " + c.getName());
                  e.printStackTrace();
               }
            }
         }
      }
   }
}

org.jboss.arquillian.core.spi.LoadableExtension

my.testsuite.CloseCustomContainersOnAfterSuiteExtension

META-INF/services/org.jboss.arquillian.core.spi.LoadableExtension placed on classpath of your testsuite.