Processing batch items in parallel

I know this is old, but if you get a few minutes, revisit your attempt to use the MSBuild task. Using the Properties and/or AdditionalProperties reserved item metadata elements* will resolve the issue you described in your code sample ("Runs only once - I guess MSBuild detects it's the same project").

The MSBuild file below processes items from an ItemGroup in parallel via MSBuild's parallel support (including /maxCpuCount). It does not use BuildTargetsInParallel from the MSBuild Extension Pack, nor any other custom or inline task.

<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">

  <Target Name="Build" >
    <ItemGroup>
      <Waits Include="3000;2000"/>
    </ItemGroup>

    <ItemGroup>
      <ProjectItems Include="$(MSBuildProjectFullPath)">
        <Properties>
          WaitMs=%(Waits.Identity)
        </Properties>
      </ProjectItems>
    </ItemGroup>
    <MSBuild Projects="@(ProjectItems)" Targets="WaitSpecifiedMs" BuildInParallel="true" />
  </Target>

  <Target Name="WaitSpecifiedMs">
    <Wait DurationMs="$(WaitMs)" />
  </Target>

</Project>

* Well-hidden under "Properties Metadata" on the MSBuild Task reference page.