I have written an AddIn for VS2003.  The AddIn opens a solution, sets
the current Configuration to Release, sets all projects to
ShouldBuild, Cleans the solution, organizes the Projects by
dependencies, and then builds each Project.

If I open a Solution with 4 projects with NO dependencies between any
projects and run the AddIn, I get repeated compiles.  Assuming the
projects are ordered Project1, Project2, Project3, and Project4:  When
I compile Project1, it builds. When I compile Project2, it will first
compile Project1 (which is Up-To-Date so it goes fast) and then
Project2 compiles.  Project3 causes an attempted compile of 1 and then
2 before 3 compiles.

I can post some more code if need be and I have a standalone AddIn
that demonstrates this issue but let me give a skeleton and see if
anyone has some ideas.  Note that Wait(true) performs a PeekMessage
loop until OnBuildDone is called and Wait(false) performs a
PeekMessage loop until ProjectBuildFinished is called but more
importantly also waits for OnBuildProjConfigDone to be called where
the 1st param matches m_csCurrentProject.

   CComPtr<EnvDTE::_Solution> pDispSolution;
   VERIFY_OK(m_pDTE->get_Solution(&pDispSolution));
   CComBSTR bszWorkspacePathName =
"C:\\CODE\\T1\\T1TEST\\T1TEST.SLN";
   VERIFY_OK(pDispSolution->Open(bszWorkspacePathName));
   {
       // set the active configuration to Release
       CComPtr<EnvDTE::Commands> pCommands;
       VERIFY_OK(m_pDTE->get_Commands(&pCommands));
       CComBSTR bszGUID = "{5EFC7975-14BC-11CF-9B2B-00AA00573819}";
       long lID = 684;
       CComVariant Vari("Release");
       CComVariant CustomOut;
       VERIFY_OK(pCommands->Raise(bszGUID, 684, &Vari, &CustomOut));
   }
   CComPtr<EnvDTE::SolutionBuild> pSolutionBuild;
   VERIFY_OK(pDispSolution->get_SolutionBuild(&pSolutionBuild));
   ... // use project dependencies to fill in m_projectCompileOrder
   ... // which is of type CAtlList<CComPtr<EnvDTE::Project>
   for (POSITION pos = m_projectCompileOrder.GetHeadPosition(); pos
!= NULL;)
   {
       CComPtr<EnvDTE::Project> pGenProject =
m_projectCompileOrder.GetNext(pos);

       CComPtr<IDispatch> pDispatch;
       VERIFY_OK(pGenProject->get_Object(&pDispatch));
       m_pVCProject = pDispatch;

       CComBSTR bszProjectFileName;
       VERIFY_OK(m_pVCProject->get_ProjectFile(&bszProjectFileName));
       m_csCurrentProject = bszProjectFileName;
       m_csCurrentProject.MakeUpper();

       CComPtr<IDispatch> pDispConfigs;
       VERIFY_OK(m_pVCProject->get_Configurations(&pDispConfigs));
       CComQIPtr<IVCCollection> pVCConfigurations(pDispConfigs);

       CComPtr<EnvDTE::SolutionConfiguration> pSolutionConfiguration;
       VERIFY_OK(pSolutionBuild->get_ActiveConfiguration(&pSolutionConfiguration));

       CComPtr<EnvDTE::SolutionContexts> pSolutionContexts;
       VERIFY_OK(pSolutionConfiguration->get_SolutionContexts(&pSolutionContexts));

       CComBSTR projectUniqueName;
       pGenProject->get_UniqueName(&projectUniqueName);

       CComPtr<EnvDTE::SolutionContext> pSolutionContext;
       pSolutionContexts->Item(CComVariant(projectUniqueName),
&pSolutionContext);

       CComBSTR bstrConfigurationName;
       VERIFY_OK(pSolutionContext->get_ConfigurationName(&bstrConfigurationName));

       CComBSTR bstrPlatformName;
       VERIFY_OK(pSolutionContext->get_PlatformName(&bstrPlatformName));

       CString configurationCombinedName =
CString(bstrConfigurationName) + "|" + CString(bstrPlatformName);
       CComBSTR bstrConfigurationCombinedName =
configurationCombinedName;

       CComPtr<IDispatch> pDispConfig;
       VERIFY_OK(pVCConfigurations->Item(CComVariant(bstrConfigurationCombinedName),
&pDispConfig));
       m_pConfig = pDispConfig;

       CComVariant VarDisp = m_pConfig;

       if (m_pVCProjectEngineEvents)
       {
           AtlTrace("Unadvise VCProjectEngineEvents SHOULD NOT HAVE
REACHED HERE!\r\n");
           VERIFY_OK(m_VCProjectEngineEventsSink.DispEventUnadvise((IUnknown*)m_pVCProjectEngineEvents.p));
           m_pVCProjectEngineEvents = NULL;
       }

       CComPtr<IDispatch> pDispProjEngine;
       VERIFY_OK(m_pVCProject->get_VCProjectEngine(&pDispProjEngine));

       CComQIPtr<VCProjectEngine> pEngine;
       pEngine = pDispProjEngine;

       CComPtr<IDispatch> pDispProjEvents;
       VERIFY_OK(pEngine->get_Events(&pDispProjEvents));
       m_pVCProjectEngineEvents = pDispProjEvents;
       if (m_pVCProjectEngineEvents)
       {
           VERIFY_OK(m_VCProjectEngineEventsSink.DispEventAdvise((IUnknown*)m_pVCProjectEngineEvents.p));
       }

       m_bInBuild = true;
       m_bInConfigBuild = true;
       VERIFY_OK(m_pConfig->Build());
       this->Wait(false);
       TRACE("After Wait for Build\r\n");

       if (m_pVCProjectEngineEvents)
       {
           TRACE("Unadvise VCProjectEngineEvents\r\n");
           VERIFY_OK(m_VCProjectEngineEventsSink.DispEventUnadvise((IUnknown*)m_pVCProjectEngineEvents.p));
           m_pVCProjectEngineEvents = NULL;
       }

       pDispProjEvents = NULL;
       pEngine = (IUnknown *)NULL;
       pDispProjEngine = NULL;

       m_pConfig = (IUnknown *)NULL;
       pDispConfig = NULL;
       pVCConfigurations = (IUnknown *)NULL;
       pSolutionContext = NULL;
       pSolutionContexts = NULL;
       pSolutionConfiguration = NULL;
       pDispConfigs = NULL;
       m_pVCProject = (IUnknown *)NULL;
       pDispatch = NULL;
       pGenProject = NULL;
   }

   this->Wait(true);
   TRACE("After Wait for OnBuildDone\r\n");
   ... // code continues closing the solution and Quitting IDE