You don't need to include the nuget.exe from the .nuget folder in your source control. If you edit the NuGet.target file the .nuget folder - which you probably did include in your source control, then'll see at about line 15 (so it was here on my machine):
<!-- Download NuGet.exe if it does not already exist -->
<DownloadNuGetExe Condition=" '$(DownloadNuGetExe)' == '' ">false</DownloadNuGetExe>
Change that to :
<!-- Download NuGet.exe if it does not already exist -->
<DownloadNuGetExe Condition=" '$(DownloadNuGetExe)' == '' ">true</DownloadNuGetExe>
And voila !
Michael