Critical Services Not Starting Automatically & Access to Server occasionally dropping out

For the last few months we have been trying to resolve an issue where access to files on the server (SBS2011 - running domain services, exchange, etc) get so slow or just unresponsive. Logging onto the server is also not possible till it starts responding
again.
We also found that when the server starts, the Netlogon services does not start automatically event though it is set to auto start. There are a number of other services mainly exchange services that do not start as well but it seems this may be due to the
net service not starting.
We have re-installed the OS but this does not seem to have fixed the issue. The environment is a mix of the SBS2011 server, two Windows Server 2003 boxes - one running Terminal Services. The other was being used for SAP but no longer in use. The clients
are mainly XP with a few Windows 7 machines. We are in the process of planning the replacement of the XP machines.

You re-installed SBS2011? - that seems rather drastic.  Did you maintain your domain or just set it all up again?
This sounds like a DNS issue but have a look at the event viewer and google/post the Event ID and Source.  Given those two you can start to track down the cause and possible fixes at www.eventid.net.  Just be aware that SBS2011 has a lot of
"normal" event errors, see http://support.microsoft.com/kb/2483007
You should also run the SBS best practice analyzer and maybe run the "Fix my network" wizard in the SBS console.  Also make sure SBS is the DHCP server for the network.
-- Al

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    #1.5 #001CC4695AD8001A000000100000079C00045DB6C93D4DAD#1228939548538#com.sap.ip.mmr.tools.RunTask##com.sap.ip.mmr.tools.RunTask#Administrator#79423####d7c673d0c6f411dd92de001cc4695ad8#SAPEngine_Application_Thread[impl:3]_33##0#0#Info##Plain###Connecting Model Repository ...#
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    #1.5 #001CC4695AD8001A000000140000079C00045DB6C93D69D0#1228939548553#com.sap.ip.mmr.tools.RunTask##com.sap.ip.mmr.tools.RunTask#Administrator#79423####d7c673d0c6f411dd92de001cc4695ad8#SAPEngine_Application_Thread[impl:3]_33##0#0#Info##Plain###Start local transaction ...#
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    #1.5 #001CC4695AD80018000000000000171400045DBBE9BCCED0#1228961568691#com.sap.engine.services.connector##com.sap.engine.services.connector######27cee540c72911ddb4ee001cc4695ad8#SAPEngine_System_Thread[impl:5]_25##0#0#Error##Plain###ResourceObjectFactory.getObjectInstance(), Error: com.sap.engine.services.connector.exceptions.BaseResourceException: ConnectionFactory "QueueConnectionFactory" does not exist. Possible reasons: the connector in which ConnectionFactory "QueueConnectionFactory" is defined is not deployed or not started.
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                    at com.sap.engine.services.jndi.implclient.ClientContext.lookup(ClientContext.java:414)
                    ... 24 more
    #1.5 #001CC4695AD80018000000030000171400045DBBE9BDBF4A#1228961568753#com.sap.engine.services.deploy##com.sap.engine.services.deploy######27cee540c72911ddb4ee001cc4695ad8#SAPEngine_System_Thread[impl:5]_25##0#0#Error#1#/System/Server#Java#deploy_5029##Exception in operation startApp with application halliburton.com/halusrgrpap.#2#startApp#halliburton.com/halusrgrpap#
    #1.5 #001CC4695AD80018000000040000171400045DBBE9BDC46C#1228961568753#com.sap.engine.services.deploy##com.sap.engine.services.deploy######27cee540c72911ddb4ee001cc4695ad8#SAPEngine_System_Thread[impl:5]_25##0#0#Error#1#/System/Audit#Java###Exception #1#com.sap.engine.services.deploy.exceptions.ServerDeploymentException: Exception in operation startApp with application halliburton.com/hal~usrgrpap.
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                    at com.sap.engine.services.ejb.message.JMSBridge.registerListener(JMSBridge.java:115)
                    ... 20 more
    Caused by: com.sap.engine.services.connector.exceptions.BaseResourceException: ConnectionFactory "QueueConnectionFactory" does not exist. Possible reasons: the connector in which ConnectionFactory "QueueConnectionFactory" is defined is not deployed or not started.
                    at com.sap.engine.services.connector.ResourceObjectFactory.getObjectInstance(ResourceObjectFactory.java:207)
                    at com.sap.engine.system.naming.provider.ObjectFactoryBuilderImpl._getObjectInstance(ObjectFactoryBuilderImpl.java:72)
                    at com.sap.engine.system.naming.provider.ObjectFactoryBuilderImpl.access$100(ObjectFactoryBuilderImpl.java:31)
                    at com.sap.engine.system.naming.provider.ObjectFactoryBuilderImpl$DispatchObjectFactory.getObjectInstance(ObjectFactoryBuilderImpl.java:210)
                    at javax.naming.spi.NamingManager.getObjectInstance(NamingManager.java:280)
                    at com.sap.engine.services.jndi.implclient.ClientContext.lookup(ClientContext.java:414)
                    ... 24 more
    #1.5 #001CC4695AD80018000000060000171400045DBBE9BE0AF5#1228961568769#com.sap.engine.services.deploy##com.sap.engine.services.deploy######27cee540c72911ddb4ee001cc4695ad8#SAPEngine_System_Thread[impl:5]_25##0#0#Error#1#/System/Server#Plain###
    Operation startApp over application halliburton.com/hal~usrgrpap finished with errors on server 105677750. For more detailed information see traces of Deploy Service.#
    #1.5 #001CC4695AD80018000000080000171400045DBBE9BE27D1#1228961568769#com.sap.engine.services.ejb##com.sap.engine.services.ejb######27cee540c72911ddb4ee001cc4695ad8#SAPEngine_System_Thread[impl:5]_25##0#0#Error#1#/System/Server#Java#ejb_2119##Exception during the initialization of container boot class com.halliburton.esg.eas.sec.prtusrgrpprocessing.MDBPrtUsrGrpProcBean0_0ContainerFP.#1#com.halliburton.esg.eas.sec.prtusrgrpprocessing.MDBPrtUsrGrpProcBean0_0ContainerFP#
    #1.5 #001CC4695AD80018000000090000171400045DBBE9BE2842#1228961568769#com.sap.engine.services.ejb##com.sap.engine.services.ejb######27cee540c72911ddb4ee001cc4695ad8#SAPEngine_System_Thread[impl:5]_25##0#0#Error#1#/System/Audit#Java###Exception #1#com.sap.engine.services.ejb.exceptions.deployment.EJBDeploymentException: Exception during the initialization of container boot class com.halliburton.esg.eas.sec.prtusrgrpprocessing.MDBPrtUsrGrpProcBean0_0ContainerFP.
                    at com.sap.engine.services.ejb.EJBAdmin.prepareLoad(EJBAdmin.java:1013)
                    at com.sap.engine.services.ejb.EJBAdmin.prepareStart(EJBAdmin.java:2443)
                    at com.sap.engine.services.deploy.server.application.StartTransaction.prepareCommon(StartTransaction.java:223)
                    at com.sap.engine.services.deploy.server.application.StartTransaction.prepareLocal(StartTransaction.java:176)
                    at com.sap.engine.services.deploy.server.application.ApplicationTransaction.makeAllPhasesLocal(ApplicationTransaction.java:365)
                    at com.sap.engine.services.deploy.server.application.ParallelAdapter.runInTheSameThread(ParallelAdapter.java:132)
                    at com.sap.engine.services.deploy.server.application.ParallelAdapter.makeAllPhasesLocalAndWait(ParallelAdapter.java:250)
                    at com.sap.engine.services.deploy.server.DeployServiceImpl.startApplicationLocalAndWait(DeployServiceImpl.java:4450)
                    at com.sap.engine.services.deploy.server.DeployServiceImpl.startApplicationsInitially(DeployServiceImpl.java:2610)
                    at com.sap.engine.services.deploy.server.DeployServiceImpl.clusterElementReady(DeployServiceImpl.java:2464)
                    at com.sap.engine.services.deploy.server.ClusterServicesAdapter.containerStarted(ClusterServicesAdapter.java:42)
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                    at com.sap.engine.services.ejb.message.MessageContainer.load(MessageContainer.java:451)
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