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regarding this, I guess it kinda depends on how the lists are stored and the 2 programs retrieving it. You can see this is an issue currently as WHD is reporting 64 Office x64 2013 updates while WTK is showing 63 updates but there's a difference of 8 files between them as well. http://drive.google.com/file/d/0B_QNEP8RAKhsVnoybE93OG02Ym8/edit?usp=sharing I would have thought it'd be something like, the list was online somewhere, with a upload date/time marker or version marker and so the tool uses the markers to determine if update is needed or not and the downloads the list if it does. regarding Kuc it works differently so there wouldn't be anyway for it to use the same folder.

Have you tried to make a build without deleting anything or disabling any services? If that works, then it would seem that your problem is with something that you are deleting or disabling that is necessary to install .NET 3.5. Cheers and Regards