java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at ru.bitel.common.bootstrap.Boot.boot(Boot.java:129)
        at ru.bitel.common.bootstrap.Boot.main(Boot.java:178)
Caused by: java.lang.NullPointerException
        at ru.bitel.bgbilling.kernel.wifi.WiFiAgent.main(WiFiAgent.java:69)
        ... 6 more

root@ubuntu:/usr/local/BGDialupWiFiAgent# ./update.sh 1 1
Starting libraries updating. Requesting to BGBillingServer lib info.
 05-15/08:48:55  INFO [main] DefaultServerSetup - Binding javax.jms.ConnectionFactory[org.apache.activemq.ActiveMQConnectionFactory@be0e27] to java:comp/env/mq/connectionFactory
 05-15/08:48:55  INFO [main] DefaultServerSetup - Init DB connection pools
mq 05-15/08:48:55  INFO [EventProcessor-init] EventProcessor - Init EventProcessor MQ connection factory...
mq 05-15/08:48:55 DEBUG [EventProcessor-init] FailoverTransport - Reconnect was triggered but transport is not started yet. Wait for start to connect the transport.
mq 05-15/08:48:55 DEBUG [EventProcessor-init] FailoverTransport - Started.
mq 05-15/08:48:55 DEBUG [EventProcessor-init] FailoverTransport - Waking up reconnect task
mq 05-15/08:48:55 DEBUG [ActiveMQ Task] FailoverTransport - urlList connectionList:[nio://10.11.1.11:61616?socketBufferSize=1000000]
mq 05-15/08:48:55 DEBUG [ActiveMQ Task] FailoverTransport - Attempting connect to: nio://10.11.1.11:61616?socketBufferSize=1000000
mq 05-15/08:48:56 DEBUG [ActiveMQ Task] WireFormatNegotiator - Sending: WireFormatInfo { version=6, properties={CacheSize=1024, CacheEnabled=true, SizePrefixDisabled=false, MaxInactivityDurationInitalDelay=10000, TcpNoDelayEnabled=true, MaxInactivityDuration=30000, TightEncodingEnabled=true, StackTraceEnabled=true}, magic=[A,c,t,i,v,e,M,Q]}
mq 05-15/08:48:56 DEBUG [ActiveMQ NIO Worker] WireFormatNegotiator - Received WireFormat: WireFormatInfo { version=6, properties={CacheSize=1024, CacheEnabled=true, SizePrefixDisabled=false, MaxInactivityDurationInitalDelay=10000, TcpNoDelayEnabled=true, MaxInactivityDuration=30000, TightEncodingEnabled=true, StackTraceEnabled=true}, magic=[A,c,t,i,v,e,M,Q]}
mq 05-15/08:48:56 DEBUG [ActiveMQ NIO Worker] WireFormatNegotiator - tcp:///10.11.1.11:61616 before negotiation: OpenWireFormat{version=6, cacheEnabled=false, stackTraceEnabled=false, tightEncodingEnabled=false, sizePrefixDisabled=false}
mq 05-15/08:48:56 DEBUG [ActiveMQ NIO Worker] WireFormatNegotiator - tcp:///10.11.1.11:61616 after negotiation: OpenWireFormat{version=6, cacheEnabled=true, stackTraceEnabled=true, tightEncodingEnabled=true, sizePrefixDisabled=false}
mq 05-15/08:48:56 DEBUG [ActiveMQ Task] FailoverTransport - Connection established
mq 05-15/08:48:56  INFO [ActiveMQ Task] FailoverTransport - Successfully connected to nio://10.11.1.11:61616?socketBufferSize=1000000
 05-15/08:48:57 DEBUG [main] EventProcessor - Add ru.bitel.bgbilling.server.util.Setup$1@1fa681c to BG.Event.ru.bitel.bgbilling.kernel.event.events.system.ModuleConfigModifiedEvent
mq 05-15/08:48:57 DEBUG [main] EventProcessor - Request, timeout 2000 : Event[bitel.billing.server.installer.event.GetLibrariesInfoEvent] moduleId: no; pluginId: no; cid: global; scid: -1; userId: -1; timestamp: -1
java.lang.NullPointerException
        at bitel.billing.server.installer.library.LibraryUpdate.getLibrariesForUpdate(LibraryUpdate.java:94)
        at bitel.billing.server.installer.library.LibraryUpdate.main(LibraryUpdate.java:119)
 05-15/08:48:59  INFO [Thread-1] EventProcessor - Shutdown EventProcessor...
 05-15/08:48:59 DEBUG [Thread-1] ActiveMQMessageConsumer - remove: ID:ubuntu-50399-1368593335701-0:1:2:1, lastDeliveredSequenceId:0

mq 05-15/08:48:57 DEBUG [main] EventProcessor - Request, timeout 2000 : Event[bitel.billing.server.installer.event.GetLibrariesInfoEvent] moduleId: no; pluginId: no; cid: global; scid: -1; userId: -1; timestamp: -1

Transport failed: java.io.EOFException

2) Время на машине , где запускаете update отличается от времени на сервере. Там сообщение посылается с timeout 5 секунд, и сервер если его время более чем на 5 секунд впереди считает что сообщение устарело и не принимает его .