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Dynamics CRM 2016 - SharePoint 2016 on premise server based integration: Invalid JWT token. Could not resolve issuer token

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Hello,

I am trying to set up server-based integration between Dynamics CRM 2016 and SharePoint 2016, both on-premise.

I was able to run through these steps without any problems:

https://technet.microsoft.com/en-us/library/dn949332.aspx

I'm using a certificate issued by an internal CA.

When it comes to enabling the integration from the CRM I see the following error:

Dynamics CRM trace shows:

[2016-12-19 11:24:23.694] Process: w3wp |Organization:47436906-957a-e611-80c2-00155d076001 |Thread:   41 |Category: ObjectModel |User: 2d013dd3-1aa3-4f38-9b75-f8df52a614b8 |Level: Error |ReqId: 00000000-0000-0000-0000-000000000000 | SharePointProxyBase.TrySharePointCallWithoutClaims  ilOffset = 0x27
	at SharePointProxyBase.TrySharePointCallWithoutClaims(String site)  ilOffset = 0x27
	at SharePointProxyBase.ValidateSharePointSite(String[] siteUrls, String& validationLog)  ilOffset = 0x137
	at SharePointProxyService.ValidateSharePointSite(String[] siteUrls, ExecutionContext context, String& validationLog)  ilOffset = 0xF4
	at RuntimeMethodHandle.InvokeMethod(Object target, Object[] arguments, Signature sig, Boolean constructor)  ilOffset = 0xFFFFFFFF
	at RuntimeMethodInfo.UnsafeInvokeInternal(Object obj, Object[] parameters, Object[] arguments)  ilOffset = 0x25
	at RuntimeMethodInfo.Invoke(Object obj, BindingFlags invokeAttr, Binder binder, Object[] parameters, CultureInfo culture)  ilOffset = 0xCF
	at LogicalMethodInfo.Invoke(Object target, Object[] values)  ilOffset = 0x4F
	at InternalOperationPlugin.Execute(IServiceProvider serviceProvider)  ilOffset = 0x57
	at V5PluginProxyStep.ExecuteInternal(PipelineExecutionContext context)  ilOffset = 0x265
	at VersionedPluginProxyStepBase.Execute(PipelineExecutionContext context)  ilOffset = 0x65
	at PipelineInstrumentationHelper.Execute(Boolean instrumentationEnabled, String stopwatchName, ExecuteWithInstrumentation action)  ilOffset = 0x2D
	at Pipeline.Execute(PipelineExecutionContext context)  ilOffset = 0xD8
	at <>c__DisplayClass1.<RunStage>b__0()  ilOffset = 0x0
	at PipelineInstrumentationHelper.Execute(Boolean instrumentationEnabled, String stopwatchName, ExecuteWithInstrumentation action)  ilOffset = 0x2D
	at MessageProcessor.RunStage(PipelineExecutionContext context, Int32 pipelineStage)  ilOffset = 0x39
	at MessageProcessor.Execute(PipelineExecutionContext context)  ilOffset = 0x1EB
	at InternalMessageDispatcher.Execute(PipelineExecutionContext context)  ilOffset = 0xE4
	at ExternalMessageDispatcher.ExecuteInternal(IInProcessOrganizationServiceFactory serviceFactory, IPlatformMessageDispatcherFactory dispatcherFactory, String messageName, String requestName, Int32 primaryObjectTypeCode, Int32 secondaryObjectTypeCode, ParameterCollection fields, CorrelationToken correlationToken, CallerOriginToken originToken, UserAuth userAuth, Guid callerId, Guid callerRegardingObjectId, UserType userType, Guid transactionContextId, Int32 invocationSource, Nullable`1 requestId, Version endpointVersion)  ilOffset = 0x22D
	at OrganizationSdkServiceInternal.ExecuteRequestRequestWithInstrumentation(OrganizationRequest request, CorrelationToken correlationToken, CallerOriginToken callerOriginToken, WebServiceType serviceType, UserAuth userAuth, Guid targetUserId, OrganizationContext context, Boolean returnResponse, Boolean checkAdminMode, Object operation, UserType targetUserType)  ilOffset = 0x28B
	at OrganizationSdkServiceInternal.ExecuteRequest(OrganizationRequest request, CorrelationToken correlationToken, CallerOriginToken callerOriginToken, WebServiceType serviceType, UserAuth userAuth, Guid targetUserId, Guid targetCallerRegardingObjectId, UserType targetUserType, OrganizationContext context, Boolean returnResponse, Boolean checkAdminMode)  ilOffset = 0x37
	at OrganizationSdkServiceInternal.ExecuteRequest(OrganizationRequest request, CorrelationToken correlationToken, CallerOriginToken callerOriginToken, WebServiceType serviceType, Boolean checkAdminMode, ExecutionContext executionContext)  ilOffset = 0x58
	at OrganizationSdkServiceInternal.Execute(OrganizationRequest request, CorrelationToken correlationToken, CallerOriginToken callerOriginToken, WebServiceType serviceType, Boolean checkAdminMode, ExecutionContext executionContext)  ilOffset = 0x28
	at InprocessServiceProxy.ExecuteCore(OrganizationRequest request)  ilOffset = 0x34
	at SandboxSdkListener.ExecuteInternal(SandboxCallInfo callInfo, SandboxSdkContext requestContext, String operation, Byte[] serializedRequest, IExecutionContext context, String& primaryEntityName)  ilOffset = 0xDA
	at SandboxSdkListener.Execute(SandboxCallInfo callInfo, SandboxSdkContext requestContext, String operation, Byte[] serializedRequest)  ilOffset = 0xC3
	at   ilOffset = 0xFFFFFFFF
	at SyncMethodInvoker.Invoke(Object instance, Object[] inputs, Object[]& outputs)  ilOffset = 0x241
	at DispatchOperationRuntime.InvokeBegin(MessageRpc& rpc)  ilOffset = 0x100
	at ImmutableDispatchRuntime.ProcessMessage5(MessageRpc& rpc)  ilOffset = 0x48
	at MessageRpc.Process(Boolean isOperationContextSet)  ilOffset = 0x62
	at Wrapper.Resume(Boolean& alreadyResumedNoLock)  ilOffset = 0x1B
	at ThreadBehavior.ResumeProcessing(IResumeMessageRpc resume)  ilOffset = 0x8
	at ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)  ilOffset = 0x70
	at ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)  ilOffset = 0x4
	at QueueUserWorkItemCallback.System.Threading.IThreadPoolWorkItem.ExecuteWorkItem()  ilOffset = 0x0
	at ThreadPoolWorkQueue.Dispatch()  ilOffset = 0xA3>Exception occured while accessing SharePoint: Unhandled Exception: System.Net.WebException: The remote server returned an error: (401) Unauthorized.

Server stack trace:
   at System.Net.HttpWebRequest.GetResponse()
   at Microsoft.SharePoint.Client.SPWebRequestExecutor.Execute()
   at Microsoft.SharePoint.Client.ClientContext.GetFormDigestInfoPrivate()
   at Microsoft.SharePoint.Client.ClientContext.EnsureFormDigest()
   at Microsoft.SharePoint.Client.ClientContext.ExecuteQuery()
   at Microsoft.Crm.ObjectModel.SharePointProxyBase.SharePointExecuteQueryMethod(CSOMCallInformation& callInformation, CSOMCallType callType, ClientContext clientContext)
   at System.Runtime.Remoting.Messaging.StackBuilderSink._PrivateProcessMessage(IntPtr md, Object[] args, Object server, Object[]& outArgs)
   at System.Runtime.Remoting.Messaging.StackBuilderSink.AsyncProcessMessage(IMessage msg, IMessageSink replySink)

Exception rethrown at [0]:
   at System.Runtime.Remoting.Proxies.RealProxy.EndInvokeHelper(Message reqMsg, Boolean bProxyCase)
   at System.Runtime.Remoting.Proxies.RemotingProxy.Invoke(Object NotUsed, MessageData& msgData)
   at Microsoft.Crm.ObjectModel.SharePointProxyBase.Async.EndInvoke(CSOMCallInformation& callInformation, IAsyncResult result)
   at Microsoft.Crm.ObjectModel.SharePointProxyBase.SharePointAsyncExecute(CSOMCallType callType)
   at Microsoft.Crm.ObjectModel.SharePointProxyBase.TrySharePointCallWithoutClaims(String site)


 SharePoint 2016 ULS log shows:

SPApplicationAuthenticationModule: Invalid token or signature. Exception: System.IdentityModel.Tokens.SecurityTokenException: Invalid JWT token. Could not resolve issuer token.
at Microsoft.IdentityModel.S2S.Tokens.JsonWebSecurityTokenHandler.ReadTokenCore(String token, Boolean isActorToken)
at Microsoft.IdentityModel.S2S.Tokens.JsonWebSecurityTokenHandler.ReadActor(IDictionary`2 payload)
at Microsoft.IdentityModel.S2S.Tokens.JsonWebSecurityTokenHandler.ReadTokenCore(String token, Boolean isActorToken)
at Microsoft.SharePoint.IdentityModel.SPApplicationAuthenticationModule.TryExtractAndValidateToken(HttpContext httpContext, SPIncomingTokenContext& tokenContext)


I've verified the Trusted Security Token Issuer:

IsSelfIssuer                  : True
NameId                        : 00000007-0000-0000-c000-000000000000@47436906-9
                                57a-e611-80c2-00155d076001
RegisteredIssuerName          : 00000007-0000-0000-c000-000000000000@47436906-9
                                57a-e611-80c2-00155d076001
AuthorizationEndPointUri      :
EndSessionEndPointUri         :
DefaultClientIdentifier       :
ScopedClientIdentifier        : {}
IdentityClaimTypeInformation  : Microsoft.SharePoint.Administration.Claims.SPTr
                                ustedClaimTypeInformation
Description                   :
SigningCertificate            : [Subject]
                                  CN=XXXXXXXXXXXXXX, OU=XX, O=XXX, L=XXXXXX,
                                S=XXXXXX, C=XX

                                [Issuer]
                                  CN=XXXXXXXXXXX, DC=XXX, DC=local

                                [Serial Number]
                                  000000F2B9CF8C79DE56EB6F12000100000000

                                [Not Before]
                                  16/12/2016 12:00:49

                                [Not After]
                                  16/12/2018 12:00:49

                                [Thumbprint]
                                  00001145E009DFCCCB5AF9856B00478873100000

AdditionalSigningCertificates : {}
MetadataEndPoint              : xxxxxxxxxx/.../metadataen
                                dpoint.svc/json?orgName=XXXXXXXXXXX
IsAutomaticallyUpdated        : True
Name                          : crm
TypeName                      : Microsoft.SharePoint.Administration.Claims.SPTr
                                ustedSecurityTokenService
DisplayName                   : crm
Id                            : 6b59addd-0cbd-4bc0-a240-8709c7f0da2f
Status                        : Online
Parent                        : SPSecurityTokenServiceManager
                                Name=SecurityTokenServiceManager
Version                       : 67798
DeploymentLocked              : False
Properties                    : {}
Farm                          : SPFarm Name=SharePoint_Config
UpgradedPersistedProperties   : {}


 Not sure  what could be causing the problem, any ideas would be appreciated!


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