Unrollback the Scons changes, they weren't the cause of the problem.

site_scons/site_tools/component_targets_msvs.py

 #!/usr/bin/python2.4
 # Copyright 2008, Google Inc.
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without
 # modification, are permitted provided that the following conditions are
 # met:
 #
 #     * Redistributions of source code must retain the above copyright
 # notice, this list of conditions and the following disclaimer.
@@ skipping 87 matching lines @@
 
   Returns:
     Zero if successful.
   """
   source = source       # Silence gpylint
 
   target_name = env['TARGET_NAME']
   project_file = target[0].path
   project_to_main = env.RelativePath(target[0].dir, env.Dir('$MAIN_DIR'),
                                      sep='/')
-  hammer_bat = '$(ProjectDir)/%s/hammer.bat' % project_to_main
+
+  env_hammer_bat = env.Clone(VS_PROJECT_TO_MAIN_DIR=project_to_main)
+  hammer_bat = env_hammer_bat.subst('$COMPONENT_VS_PROJECT_SCRIPT_PATH', raw=1)
 
   # Project header
   xml_impl = xml.dom.getDOMImplementation()
   doc = xml_impl.createDocument(None, 'VisualStudioProject', None)
 
   n_root = doc.documentElement
   n_root.setAttribute('ProjectType', 'Visual C++')
   n_root.setAttribute('Version', '8.00')
   n_root.setAttribute('Name', target_name)
   n_root.setAttribute('ProjectGUID', MakeGuid(target_name))
@@ skipping 307 matching lines @@
     return
 
   # Include tools we need
   env.Tool('gather_inputs')
 
   env.SetDefault(
       COMPONENT_VS_SOLUTION_DIR='$DESTINATION_ROOT/solution',
       COMPONENT_VS_PROJECT_DIR='$COMPONENT_VS_SOLUTION_DIR/projects',
       COMPONENT_VS_SOLUTION_SUFFIX='.sln',
       COMPONENT_VS_PROJECT_SUFFIX='.vcproj',
+      COMPONENT_VS_PROJECT_SCRIPT_NAME = 'hammer.bat',
+      COMPONENT_VS_PROJECT_SCRIPT_PATH = (
+          '$$(ProjectDir)/$VS_PROJECT_TO_MAIN_DIR/'
+          '$COMPONENT_VS_PROJECT_SCRIPT_NAME'),
   )
 
   AddTargetGroup('all_solutions', 'solutions can be built')
 
   # Add builders
   vcprojaction = SCons.Script.Action(ComponentVSProjectBuilder, varlist=[
       'TARGET_NAME',
       'TARGET_PATH',
+      'COMPONENT_VS_PROJECT_SCRIPT_PATH',
   ])
   vcprojbuilder = SCons.Script.Builder(
       action=vcprojaction,
       suffix='$COMPONENT_VS_PROJECT_SUFFIX')
 
   slnaction = SCons.Script.Action(ComponentVSSolutionBuilder, varlist=[
       'SOLUTION_TARGETS',
       'SOLUTION_FOLDERS',
       'SOLUTION_PROJECTS',
   ])
   slnbuilder = SCons.Script.Builder(
       action=slnaction,
       suffix='$COMPONENT_VS_SOLUTION_SUFFIX')
 
   env.Append(BUILDERS={
       'ComponentVSProjectBuilder': vcprojbuilder,
       'ComponentVSSolutionBuilder': slnbuilder,
   })