Why doesn't my .wpp.targets file get applied on my build server?

I have a custom .wpp.targets file which is setting some ACL's. When I build from within visual studio, the source manifest file that is generated contains the custom ACL's.

When I run from my build server, it just doesn't work. The generated file does not contain the acl's out of the .wpp.targets file.

The build server has .net framework 4 installed, web deploy, it has the correct Microsoft.Web.Publishing.targets file. I have included some diagnostics from the build on the server where it seems that the "AfterAddIisSettingAndFileContentsToSourceManifest" property is false. I'm not familiar with msbuild though. Can anyone help?

EDIT:

I noticed that in my Microsoft.Web.Publishing.targets there is the following lines:

  <PropertyGroup>
    <WebPublishPipelineCustomizeTargetFile Condition="'$(WebPublishPipelineCustomizeTargetFile)'==''">$(WebPublishPipelineProjectDirectory)\$(WebPublishPipelineProjectName).wpp.targets</WebPublishPipelineCustomizeTargetFile>
  </PropertyGroup>

  <Import Project="$(WebPublishPipelineCustomizeTargetFile)" Condition="Exists($(WebPublishPipelineCustomizeTargetFile))"/>

However there is nothing about the webpublishpipeline in the output from msbuild. I don't think my .wpp.targets file is even being looked at!

The targets file:

<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003"  ToolsVersion="4.0">
    <!--
    ********************************************************************
     Task Custom ACLs 
    ********************************************************************
    -->
    <PropertyGroup>
         <!-- Extends the AfterAddIisSettingAndFileContentsToSourceManifest action to also set ACLs-->
           <AfterAddIisSettingAndFileContentsToSourceManifest Condition="'$(AfterAddIisSettingAndFileContentsToSourceManifest)'==''">
                $(AfterAddIisSettingAndFileContentsToSourceManifest);
                SetCustomACLs;
            </AfterAddIisSettingAndFileContentsToSourceManifest>
        </PropertyGroup>

        <Target Name="SetCustomACLs">
            <Message Text="Adding Custom ACls" />
            <ItemGroup>
                <!--Make sure the by default Networkservice/AppPoolIdentity have write permission to the root-->
                <MsDeploySourceManifest Include="setAcl" >
                    <Path>$(_MSDeployDirPath_FullPath)\bin\ABCpdf8-64.dll</Path>
                    <setAclAccess>ReadAndExecute</setAclAccess>
                    <setAclResourceType>File</setAclResourceType>
                    <AdditionalProviderSettings>setAclResourceType;setAclAccess</AdditionalProviderSettings>
                </MsDeploySourceManifest>
            </ItemGroup>
        </Target>
    </Project>

The msbuild output:

[GenerateMsdeployManifestFiles] CallTarget
    [22:13:44]: [CallTarget] Target "PipelinePreDeployCopyAllFilesToOneFolder" skipped. Previously built successfully.
    [22:13:44]: [CallTarget] Target "GenerateMsDeployManifestSettings" skipped. Previously built successfully.
    [22:13:44]: [CallTarget] Target "PipelinePreDeployCopyAllFilesToOneFolder" skipped. Previously built successfully.
    [22:13:44]: [CallTarget] Target "GenerateMsDeployManifestSettings" skipped. Previously built successfully.
    [22:13:44]: [CallTarget] Target "AddIis7ToSourceManifest" skipped, due to false condition; ($(_DeploymentUseIis) And ($(LocalIisVersion) >= '7')) was evaluated as (False And (7 >= '7')).
    [22:13:44]: [CallTarget] Target "AddIis6ToSourceManifest" skipped, due to false condition; ($(_DeploymentUseIis) And ($(LocalIisVersion) < '7') ) was evaluated as (False And (7 < '7') ).
    [22:13:44]: [CallTarget] AddContentPathToSourceManifest
    [22:13:44]: [AddContentPathToSourceManifest] Using "GetDeployManagedRuntimeVersion" task from assembly "C:\Program Files (x86)\MSBuild\Microsoft\VisualStudio\v10.0\Web\Microsoft.Web.Publishing.Tasks.dll".
    [22:13:44]: [AddContentPathToSourceManifest] Task "CallTarget" skipped, due to false condition; ('$(AfterAddContentPathToSourceManifest)' != '') was evaluated as ('' != '').
    [22:13:44]: [CallTarget] AddIisSettingAndFileContentsToSourceManifest
    [22:13:44]: [AddIisSettingAndFileContentsToSourceManifest] Task "CallTarget" skipped, due to false condition; ('$(AfterAddIisSettingAndFileContentsToSourceManifest)' != '') was evaluated as ('' != '').
    [22:13:44]: [CallTarget] Target "CollectDatabasesToPublish" skipped, due to false condition; ($(PublishDatabases)) was evaluated as (false).
    [22:13:44]: [CallTarget] AddDatabasesToSourceManifest
    [22:13:44]: [AddDatabasesToSourceManifest] Task "CallTarget" skipped, due to false condition; ('$(AfterAddDatabasesToSourceManifest)' != '') was evaluated as ('' != '').
    [22:13:44]: [CallTarget] WriteItemsToSourceManifest
    [22:13:44]: [WriteItemsToSourceManifest] Using "ExportManifestFile" task from assembly "C:\Program Files (x86)\MSBuild\Microsoft\VisualStudio\v10.0\Web\Microsoft.Web.Publishing.Tasks.dll".
    [22:13:44]: [WriteItemsToSourceManifest] Task "CallTarget" skipped, due to false condition; ('$(AfterWriteItemsToSourceManifest)' != '') was evaluated as ('' != '').

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