Don't use pub_packages for running the Windows pub script.

sdk/bin/pub.bat

 @echo off
 REM Copyright (c) 2014, the Dart project authors.  Please see the AUTHORS file
 REM for details. All rights reserved. Use of this source code is governed by a
 REM BSD-style license that can be found in the LICENSE file.
 
 rem Run pub.dart on the Dart VM. This script is only used when running pub from
 rem within the Dart source repo. The shipped SDK instead uses "pub_sdk.bat",
 rem which is renamed to "pub.bat" when the SDK is built.
 
 setlocal
@@ skipping 13 matching lines @@
 set VM_OPTIONS=
 
 rem Give the VM extra memory for dart2js.
 rem # TODO(rnystrom): Remove when #8355 is fixed.
 rem See comments regarding options below in dart2js shell script.
 set VM_OPTIONS=%VM_OPTIONS% --old_gen_heap_size=1024
 
 rem Use the Dart binary in the built SDK so pub can find the version file next
 rem to it.
 set BUILD_DIR=%SDK_DIR%\..\build\ReleaseIA32
-set PACKAGES_DIR=%BUILD_DIR%\pub_packages
+set PACKAGES_DIR=%BUILD_DIR%\packages
 set DART=%BUILD_DIR%\dart-sdk\bin\dart
 
 rem Run the async/await compiled pub.
 set PUB="%SDK_DIR%\lib\_internal\pub_generated\bin\pub.dart"
 "%DART%" %VM_OPTIONS% --package-root="%PACKAGES_DIR%" "%PUB%" %*
 
 endlocal
 
 exit /b %errorlevel%
 
 :follow_links
 setlocal
 for %%i in (%1) do set result=%%~fi
 set current=
 for /f "usebackq tokens=2 delims=[]" %%i in (`dir /a:l "%~dp1" 2^>nul ^
                                              ^| find ">     %~n1 ["`) do (
   set current=%%i
 )
 if not "%current%"=="" call :follow_links "%current%", result
 endlocal & set %~2=%result%
 goto :eof
 
 :end