"java.net.ConnectException: JBAS012144: Could not connect to remote://localhost:6999. The connection timed out" when trying to upgrade JBoss ON 3.2

Issue

• We are trying to upgrade JBoss ON 3.2 and to install Red Hat JBoss Operations Network 3.2 Update 01 but the update fails with the following:

$ ./apply-updates.sh /opt/jboss/jon/jon-server-3.2.0.GA/
        Successfully detected server [/opt/jboss/jon/jon-server-3.2.0.GA/] to be upgraded. Proceeding...
        Proceeding with application of patch '01' to /opt/jboss/jon/jon-server-3.2.0.GA/
        Successfully detected agent [/opt/jboss/jon/rhq-agent] to be upgraded. Proceeding...
        Proceeding with application of patch '01' to /opt/jboss/jon/rhq-agent
        Verifying that all [Server] component(s) are stopped...
        Successfull verified that [Server] is already shut down.
        Archiving legacy files. This list is cumulative and may attempt to remove files handled by earlier updates.
        Moving the following files to [./.old] for server and/or [./.old-agent] for agent:
        See './update.log' for more archive details.
        Applying the update contents.
        Applying additional JON Server updates...
        Starting JON Server...
        Starting JBoss CLI and applying patches...
org.jboss.as.cli.CliInitializationException: Failed to connect to the controller
        at org.jboss.as.cli.impl.CliLauncher.initCommandContext(CliLauncher.java:280)
        at org.jboss.as.cli.impl.CliLauncher.main(CliLauncher.java:240)
        at org.jboss.as.cli.CommandLineMain.main(CommandLineMain.java:34)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:601)
        at org.jboss.modules.Module.run(Module.java:270)
        at org.jboss.modules.Main.main(Main.java:411)
Caused by: org.jboss.as.cli.CommandLineException: The controller is not available at localhost:6999
        at org.jboss.as.cli.impl.CommandContextImpl.tryConnection(CommandContextImpl.java:951)
        at org.jboss.as.cli.impl.CommandContextImpl.connectController(CommandContextImpl.java:790)
        at org.jboss.as.cli.impl.CommandContextImpl.connectController(CommandContextImpl.java:766)
        at org.jboss.as.cli.impl.CliLauncher.initCommandContext(CliLauncher.java:278)
        ... 8 more
Caused by: java.io.IOException: java.net.ConnectException: JBAS012144: Could not connect to remote://localhost:6999. The connection timed out
        at org.jboss.as.controller.client.impl.AbstractModelControllerClient.executeForResult(AbstractModelControllerClient.java:129)
        at org.jboss.as.controller.client.impl.AbstractModelControllerClient.execute(AbstractModelControllerClient.java:71)
        at org.jboss.as.cli.impl.CommandContextImpl.tryConnection(CommandContextImpl.java:929)
        ... 11 more
Caused by: java.net.ConnectException: JBAS012144: Could not connect to remote://localhost:6999. The connection timed out
        at org.jboss.as.protocol.ProtocolConnectionUtils.connectSync(ProtocolConnectionUtils.java:131)
        at org.jboss.as.protocol.ProtocolConnectionManager$EstablishingConnection.connect(ProtocolConnectionManager.java:256)
        at org.jboss.as.protocol.ProtocolConnectionManager.connect(ProtocolConnectionManager.java:70)
        at org.jboss.as.protocol.mgmt.FutureManagementChannel$Establishing.getChannel(FutureManagementChannel.java:176)
        at org.jboss.as.cli.impl.CLIModelControllerClient.getOrCreateChannel(CLIModelControllerClient.java:156)
        at org.jboss.as.cli.impl.CLIModelControllerClient$2.getChannel(CLIModelControllerClient.java:118)
        at org.jboss.as.protocol.mgmt.ManagementChannelHandler.executeRequest(ManagementChannelHandler.java:115)
        at org.jboss.as.protocol.mgmt.ManagementChannelHandler.executeRequest(ManagementChannelHandler.java:90)
        at org.jboss.as.controller.client.impl.AbstractModelControllerClient.executeRequest(AbstractModelControllerClient.java:236)
        at org.jboss.as.controller.client.impl.AbstractModelControllerClient.execute(AbstractModelControllerClient.java:141)
        at org.jboss.as.controller.client.impl.AbstractModelControllerClient.executeForResult(AbstractModelControllerClient.java:127)
        ... 13 more
        Stopping the JON Server...

        You have successfully extracted patch contents into (JON server) and/or (JON agent) installation folder(s).
        You should do the following as is necessary:
         i)Closely follow the remainder of the instructions delivered with this update.
         ii)restart your server(s)*
         iii)restart agents and request agent updates
         NOTE: for HA environments you may need to repeat the steps here for each server before patch application is complete.