Resolution:
This set of log messages at an INFO/WARN level are innocuous and can be ignored. Also, the WARN level logs have been changed to DEBUG in AMX BPM v2.1.0 hotfix 11.
The following is an example from the BPM.log. 

===============
07 Nov 2014 16:13:35,566 [PVM:DB Process Worker:8] [INFO ] stdout - ***WARNING*** non conforming messages
07 Nov 2014 16:13:35,569 [PVM:DB Process Worker:8] [INFO ] stdout - java.lang.Thread.getStackTrace(Thread.java:1479)
07 Nov 2014 16:13:35,569 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.bx.n2.ec.BxN2Logger.printStackTraces(BxN2Logger.java:290)
07 Nov 2014 16:13:35,569 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.bx.n2.ec.BxN2Logger.event(BxN2Logger.java:183)
07 Nov 2014 16:13:35,569 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.bx.n2.ec.BxN2Logger.warn(BxN2Logger.java:115)
07 Nov 2014 16:13:35,569 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.bx.core.behaviors.activity.BxActivityCompletionNotifierImpl.setReady(BxActivityCompletionNotifierImpl.java:34)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.n2.ut.core.handler.StartGroupPayloadHandler.handlePayload(StartGroupPayloadHandler.java:109)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.n2.ut.core.UserActivity.postEval(UserActivity.java:392)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.bx.core.behaviors.activity.BxExtensionBehavior.doExternal(BxExtensionBehavior.java:209)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.bx.core.behaviors.activity.BxActivityBaseBehavior.handleModelEvent(BxActivityBaseBehavior.java:983)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.bx.core.behaviors.activity.BxActivityBaseBehavior.handleModelEvent(BxActivityBaseBehavior.java:1)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.pvm.infra.api.impl.util.director.IpmEventDirectorBase.handleModelEvent(IpmEventDirectorBase.java:158)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.pvm.infra.api.impl.util.director.IpmEventDirectorBase.handleEvent(IpmEventDirectorBase.java:89)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.pvm.infra.support.work.impl.WorkItemAbstract.execute(WorkItemAbstract.java:109)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.pvm.db.persist.services.engine.IdbSTWorkRunnable.doWorkBlock(IdbSTWorkRunnable.java:96)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - com.tibco.pvm.infra.services.engine.impl.STWorkRunnable.run(STWorkRunnable.java:48)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
07 Nov 2014 16:13:35,570 [PVM:DB Process Worker:8] [INFO ] stdout - java.lang.Thread.run(Thread.java:662)
07 Nov 2014 16:13:35,571 [PVM:DB Process Worker:8] [WARN ] com.tibco.bx.core.BxSystemImpl - [WARN] - {BX_ID} - setReady: scheduling external event to a task with uri: pvm:001i14grn6; userData: Group id mapping: _nqqYUI1wEeKb5JiJxJ0JEw -> 115046 ¬{correlationId=``, principalName=`user01`, threadId=`1146`, componentClassName=`com.tibco.bx.core.BxSystemImpl`, hostAddress=`0.0.0.0`, compositeApplicationName=`amx.bpm.app`, nodeName=`BPMNode`, severity=`WARN`, eventType=`MESSAGE`, componentId=`BX`, message=`setReady: scheduling external event to a task with uri: pvm:001i14grn6; userData: Group id mapping: _nqqYUI1wEeKb5JiJxJ0JEw -> 115046`, threadName=`PVM:DB Process Worker:8`, principalId=`0718263C-2165-4B79-B03C-5298ADD885B8`, priority=`MEDIUM`, environmentName=`BPMEnvironment`, hostName=`host01`, creationTime=`2014-11-07T16:13:35.571-0500`, messageId=`BX_ID`, ¬}
07 Nov 2014 16:13:36,283 [amxbpm_pm_tp_8] [INFO ] stdout - ***WARNING*** non conforming messages
07 Nov 2014 16:13:36,283 [amxbpm_pm_tp_8] [INFO ] stdout - java.lang.Thread.getStackTrace(Thread.java:1479)
07 Nov 2014 16:13:36,283 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.bx.n2.ec.BxN2Logger.printStackTraces(BxN2Logger.java:290)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.bx.n2.ec.BxN2Logger.event(BxN2Logger.java:183)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.bx.n2.ec.BxN2Logger.warn(BxN2Logger.java:115)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.bx.core.behaviors.activity.BxActivityCompletionNotifierImpl.setReady(BxActivityCompletionNotifierImpl.java:34)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.n2.ut.core.api.impl.NotificationServiceHandler.setPostEvalRequest(NotificationServiceHandler.java:219)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.n2.ut.core.api.impl.NotificationServiceHandler.scheduleWorkItemWithModelResponse(NotificationServiceHandler.java:157)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - sun.reflect.GeneratedMethodAccessor1096.invoke(Unknown Source)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - java.lang.reflect.Method.invoke(Method.java:597)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.amf.platform.runtime.componentframework.internal.proxies.operation.OperationHandler$1.run(OperationHandler.java:589)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - java.security.AccessController.doPrivileged(Native Method)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - javax.security.auth.Subject.doAs(Subject.java:337)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.amf.platform.runtime.componentframework.internal.proxies.operation.OperationHandler.invokeMethodWithThreadContext(OperationHandler.java:575)
07 Nov 2014 16:13:36,284 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.amf.platform.runtime.componentframework.internal.proxies.operation.AsyncToSyncOperationHandler.invoke(AsyncToSyncOperationHandler.java:90)
07 Nov 2014 16:13:36,285 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.amf.platform.runtime.componentframework.internal.proxies.ProxyInvocationHandlerRegistry$ProxyInvocationContext.invoke(ProxyInvocationHandlerRegistry.java:442)
07 Nov 2014 16:13:36,285 [amxbpm_pm_tp_8] [INFO ] stdout - $Proxy36.onRemoteMessage(Unknown Source)
07 Nov 2014 16:13:36,285 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.amf.platform.runtime.componentframework.internal.messagingbus.ems.inbound.AbstractMessagingContext.run(AbstractMessagingContext.java:130)
07 Nov 2014 16:13:36,285 [amxbpm_pm_tp_8] [INFO ] stdout - com.tibco.amf.platform.runtime.componentframework.internal.messagingbus.ems.inbound.xa.XAMessagingContext.run(XAMessagingContext.java:74)
07 Nov 2014 16:13:36,285 [amxbpm_pm_tp_8] [INFO ] stdout - java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
07 Nov 2014 16:13:36,285 [amxbpm_pm_tp_8] [INFO ] stdout - java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
07 Nov 2014 16:13:36,285 [amxbpm_pm_tp_8] [INFO ] stdout - java.lang.Thread.run(Thread.java:662)
07 Nov 2014 16:13:36,286 [amxbpm_pm_tp_8] [WARN ] com.tibco.bx.core.BxSystemImpl - [WARN] - {BX_ID} - setReady: scheduling external event to a task with uri: pvm:001i14grn6; userData: <xml-fragment>
  <messageDetails>
    <workItemId id="243475"/>
    <activityID>pvm:001i14grn6</activityID>
    <uaSequenceId>1</uaSequenceId>
    <brmSequenceId>1</brmSequenceId>
  </messageDetails>
</xml-fragment> ¬{correlationId=`5be9056f-8f02-46bd-835d-52a71187278e`, threadId=`4320`, componentClassName=`com.tibco.bx.core.BxSystemImpl`, requestReceived=`Fri Nov 07 16:13:36 EST 2014`, parentContextId=`5be9056f-8f02-46bd-835d-52a71187278e`, hostAddress=`0.0.0.0`, compositeApplicationName=`amx.bpm.app`, nodeName=`BPMNode`, severity=`WARN`, eventType=`MESSAGE`, componentId=`BX`, serviceName=`servicename`, message=`setReady: scheduling external event to a task with uri: pvm:001i14grn6; userData: <xml-fragment>
  <messageDetails>
    <workItemId id="243475"/>
    <activityID>pvm:001i14grn6</activityID>
    <uaSequenceId>1</uaSequenceId>
    <brmSequenceId>1</brmSequenceId>
  </messageDetails>
</xml-fragment>`, contextId=`c50fb676-9ed3-4eed-bea6-dd7450426fe5`, threadName=`amxbpm_pm_tp_8`, priority=`MEDIUM`, environmentName=`BPMEnvironment`, hostName=`host01`, creationTime=`2014-11-07T16:13:36.286-0500`, messageId=`BX_ID`, ¬}
===============

After applying TIBCO ActiveMatrix BPM v2.1.0 hotfix 10, the logs contain - "***WARNING*** non conforming messages".