Hi Linda.
Thanks for the reply. As far as I can see all pages are published. I will try creating the User Policy and see what happens.
In the meantime I have enabled verbose logging and pulled this out:
11/22/2013 08:50:03.93 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation Database tzku Verbose ConnectionString: 'Data Source=SQLServer\Intranet;Initial Catalog=WSS_Content;Integrated Security=True;Enlist=False;Asynchronous
Processing=False;Connect Timeout=15' ConnectionState: Closed ConnectionTimeout: 15 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8xfr Verbose PermissionMask check failed. asking for 0x4000000000000000, have 0x00000000 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8xfr Verbose PermissionMask check failed. asking for 0x00000001, have 0x00000000 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8xfr Verbose PermissionMask check failed. asking for 0x00000005, have 0x00000000 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8xfr Verbose PermissionMask check failed. asking for 0x00000015, have 0x00000000 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8xfr Verbose PermissionMask check failed. asking for 0x00000041, have 0x00000000 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8xfr Verbose PermissionMask check failed. asking for 0x08000000, have 0x00000000 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8xfr Verbose PermissionMask check failed. asking for 0x00000001, have 0x00000000 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8xfr Verbose PermissionMask check failed. asking for 0x00000005, have 0x00000000 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8xfr Verbose PermissionMask check failed. asking for 0x00000015, have 0x00000000 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8xfr Verbose PermissionMask check failed. asking for 0x00000041, have 0x00000000 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8xfr Verbose PermissionMask check failed. asking for 0x00010000, have 0x00000000 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8e2s Medium Unknown SPRequest error occurred. More information: 0x80070005 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General ftd0 Verbose Access Denied. Exception: System.UnauthorizedAccessException: Access is denied. (Exception from HRESULT: 0x80070005 (E_ACCESSDENIED))
at Microsoft.SharePoint.Library.SPRequestInternalClass.GetListsWithCallback(String bstrUrl, Guid foreignWebId, String bstrListInternalName, Int32 dwBaseType, Int32 dwBaseTypeAlt, Int32 dwServerTemplate, UInt32 dwGetListFlags, UInt32 dwListFilterFlags, Boolean
bPrefetchMetaData, Boolean bSecurityTrimmed, Boolean bGetSecurityData, Boolean bPrefetchRelatedFields, ISP2DSafeArrayWriter p2DWriter, Int32& plRecycleBinCount) at Microsoft.SharePoint.Library.SPRequest.GetListsWithCallback(String
bstrUrl, Guid foreignWebId, String bstrListInternalName, Int32 dwBaseType, Int32 dwBaseTypeAlt, Int32 dwServerTemplate, UInt32 dwGetListFlags, UInt32 dwListFilterFlags, Boolean bPrefetchMetaData, Boolean bSecurityTrimmed, Boolean bGetSecurityData, Boolean
bPrefetchRelatedFields, ISP2DSafeArrayWriter p2DWriter, Int32& plRecycleBinCount). 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
11/22/2013 08:50:03.94 w3wp.exe (0x2AF4) 0x272C SharePoint Foundation General 8gs1 Verbose Access Denied for /_Layouts/sitemanager.aspx?Source={WebUrl}_layouts/settings.aspx. StackTrace: at Microsoft.SharePoint.Utilities.SPUtility.HandleAccessDenied(HttpContext
context) at Microsoft.SharePoint.Utilities.SPUtility.HandleAccessDenied(Exception ex) at Microsoft.SharePoint.Library.SPRequest.GetListsWithCallback(String bstrUrl, Guid foreignWebId, String bstrListInternalName,
Int32 dwBaseType, Int32 dwBaseTypeAlt, Int32 dwServerTemplate, UInt32 dwGetListFlags, UInt32 dwListFilterFlags, Boolean bPrefetchMetaData, Boolean bSecurityTrimmed, Boolean bGetSecurityData, Boolean bPrefetchRelatedFields, ISP2DSafeArrayWriter p2DWriter, Int32&
plRecycleBinCount) at Microsoft.SharePoint.SPListCollection.EnsureListsData(Guid webId, String strListName) at Microsoft.SharePoint.SPListCollection.ItemByInternalName(String strInternalName, Boolean bThrowException)
at Microsoft.SharePoint.SPListCollection.get_Item(Guid uniqueID) at Microsoft.SharePoint.Publishing.CommonUtilities.GetListByID(SPWeb web, Guid listID, Boolean attemptCleanup) at Microsoft.SharePoint.Publishing.Internal.CachedVariationSettings.GetVariationLabelsList(SPWeb
rootWeb) at Microsoft.SharePoint.Publishing.Internal.CachedVariationSettings..ctor(Guid siteId, SPUrlZone zone) at Microsoft.SharePoint.Publishing.Internal.CachedVariationSettings.<>c__DisplayClass1.<CreateVariationSettings>b__0()
at Microsoft.SharePoint.SPSecurity.<>c__DisplayClass4.<RunWithElevatedPrivileges>b__2() at Microsoft.SharePoint.Utilities.SecurityContext.RunAsProcess(CodeToRunElevated secureCode) at Microsoft.SharePoint.SPSecurity.RunWithElevatedPrivileges(WaitCallback
secureCode, Object param) at Microsoft.SharePoint.SPSecurity.RunWithElevatedPrivileges(CodeToRunElevated secureCode) at Microsoft.SharePoint.Publishing.Internal.CachedVariationSettings.CreateVariationSettings(Guid
siteId, SPUrlZone zone, Boolean forceRefresh) at Microsoft.SharePoint.Publishing.PublishingWeb.GetVariationRootPublishingWebUrl() at Microsoft.SharePoint.Publishing.PublishingWeb.EnsureVariationInfo()
at Microsoft.SharePoint.Publishing.PublishingWeb.get_IsVariationHome() at Microsoft.SharePoint.Publishing.Internal.WebControls.ObjectSerializer.evaluateIconInfo() at Microsoft.SharePoint.Publishing.Internal.WebControls.ObjectSerializer.get_IconUrl()
at Microsoft.SharePoint.Publishing.Internal.WebControls.EcbEnabledTreeNode..ctor(EcbEnabledTreeView owner, PublishingWeb area) at Microsoft.SharePoint.Publishing.Internal.WebControls.SMTreeView.CreateNode(PublishingWeb area, EcbEnabledTreeNode
parent) at Microsoft.SharePoint.Publishing.Internal.WebControls.EcbEnabledTreeView.populateWeb(TreeNode parentNode) at Microsoft.SharePoint.Publishing.Internal.WebControls.EcbEnabledTreeView.OnTreeNodePopulate(TreeNodeEventArgs
e) at Microsoft.SharePoint.Publishing.Internal.WebControls.EcbEnabledTreeView.ExpandTreeNode(TreeNode treeNode) at Microsoft.SharePoint.Publishing.Internal.CodeBehind.SmtMainPage.TreeView_ContextChanged(Object
sender, SmtContextChangedEventArgs e) at Microsoft.SharePoint.Publishing.Internal.WebControls.SMTreeView.raiseContextChanged(SmtContextChangedEventArgs e) at Microsoft.SharePoint.Publishing.Internal.WebControls.SMTreeView.OnSelectedNodeChanged(EventArgs
e) at Microsoft.SharePoint.Publishing.Internal.WebControls.EcbEnabledTreeView.initialLoadMakeDefaultSelection(TreeNode rootNode) at Microsoft.SharePoint.Publishing.Internal.WebControls.EcbEnabledTreeView.OnLoad(EventArgs
e) at Microsoft.SharePoint.Publishing.Internal.WebControls.SMTreeView.OnLoad(EventArgs e) at System.Web.UI.Control.LoadRecursive() at System.Web.UI.Control.LoadRecursive()
at System.Web.UI.Control.LoadRecursive() at System.Web.UI.Control.LoadRecursive() at System.Web.UI.Page.ProcessRequestMain(Boolean includeStagesBeforeAsyncPoint, Boolean includeStagesAfterAsyncPoint)
at System.Web.UI.Page.ProcessRequest(Boolean includeStagesBeforeAsyncPoint, Boolean includeStagesAfterAsyncPoint) at System.Web.UI.Page.ProcessRequest() at System.Web.UI.Page.ProcessRequest(HttpContext context)
at ASP._layouts_sitemanager_aspx.ProcessRequest(HttpContext context) at System.Web.HttpApplication.CallHandlerExecutionStep.System.Web.HttpApplication.IExecutionStep.Execute() at System.Web.HttpApplication.ExecuteStep(IExecutionStep
step, Boolean& completedSynchronously) at System.Web.HttpApplication.PipelineStepManager.ResumeSteps(Exception error) at System.Web.HttpApplication.BeginProcessRequestNotification(HttpContext context, AsyncCallback
cb) at System.Web.HttpRuntime.ProcessRequestNotificationPrivate(IIS7WorkerRequest wr, HttpContext context) at System.Web.Hosting.PipelineRuntime.ProcessRequestNotificationHelper(IntPtr managedHttpContext, IntPtr
nativeRequestContext, IntPtr moduleData, Int32 flags) at System.Web.Hosting.PipelineRuntime.ProcessRequestNotification(IntPtr managedHttpContext, IntPtr nativeRequestContext, IntPtr moduleData, Int32 flags) at
System.Web.Hosting.PipelineRuntime.ProcessRequestNotificationHelper(IntPtr managedHttpContext, IntPtr nativeRequestContext, IntPtr moduleData, Int32 flags) at System.Web.Hosting.PipelineRuntime.ProcessRequestNotification(IntPtr managedHttpContext,
IntPtr nativeRequestContext, IntPtr moduleData, Int32 flags) 2ef7829e-e4c4-4fd1-a086-bb670ca22b56
However, I am yet to determine exactly what I am denied access to. Any further thoughts welcome.