pitoloko

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

I were in the same problem of you and I've developed time ago a mini-tool in .NET (VB) to solve that issue.
You can compile this Class into an exe and just run the compiled exe, the entire desktop is shown not only a explorer window like happened using CMD.
But my program is not for restart explorer, it don't kills explorer, it just start it, so if you want to kill explorer then you need to write that isntruction (in Batch for example using TaskKill command like you was using in your example).
PS: If you want the program compiled then here is: http://www.mediafire.com/download/olj659v29ao8gdv/InitializeExplorer.exe
The source is just a CLI app with a Module containning these lines:
' By Elektro
#Region " Imports "
Imports System.IO
Imports System.Runtime.InteropServices
Imports InitializeExplorer.NativeMethods
#End Region
'''
''' Initializes a new instance of Explorer process.
'''
Module InitializeExplorer
#Region " P/Invoke "
'''
''' Class NativeMethods.
'''
Friend Class NativeMethods
'''
''' Retrieves a handle to the top-level window whose class name and window name match the specified strings.
''' This function does not search child windows.
''' This function does not perform a case-sensitive search.
'''
'''
''' The class name or a class atom created by a previous call to the
''' RegisterClass or RegisterClassEx function.
''' The atom must be in the low-order word of lpClassName;
''' the high-order word must be zero.
''' If lpClassName points to a string, it specifies the window class name.
''' The class name can be any name registered with RegisterClass or RegisterClassEx,
''' or any of the predefined control-class names.
''' If lpClassName is NULL, it finds any window whose title matches the lpWindowName parameter.
'''
'''
''' The window name (the window's title).
''' If this parameter is NULL, all window names match.
''' IntPtr.
Public Shared Function FindWindowByClass(
ByVal lpClassName As String,
ByVal zero As IntPtr
) As IntPtr
End Function
End Class
#End Region
#Region " ReadOnly Strings "
'''
''' Indicates the directory where the Explorer process is located.
'''
Private ReadOnly ExplorerDirectory As String =
Environment.GetFolderPath(Environment.SpecialFolder.Windows)
'''
''' Indicates the filename of the process.
'''
Private ReadOnly ExplorerFilename As String = "Explorer.exe"
'''
''' Indicates the desk Taskbar Class-name.
'''
Private ReadOnly TaskBarClassName As String = "Shell_TrayWnd"
#End Region
#Region " Process "
'''
''' The explorer process.
'''
Dim Explorer As New Process With
{
.StartInfo = New ProcessStartInfo With
{
.FileName = Path.Combine(ExplorerDirectory, ExplorerFilename),
.WorkingDirectory = My.Application.Info.DirectoryPath,
.UseShellExecute = True,
.CreateNoWindow = True
}
}
#End Region
#Region " Main "
'''
''' Defines the entry point of the application.
'''
Sub Main()
Select Case Convert.ToBoolean(CInt(FindWindowByClass(TaskBarClassName, Nothing)))
Case False ' The Taskbar is not found.
Try
Explorer.Start()
Console.WriteLine("Windows Explorer has been re-initialized successfully")
Environment.Exit(0)
Catch ex As Exception
Console.WriteLine(ex.Message)
Debug.WriteLine(ex.Message)
Environment.Exit(1)
End Try
Case True ' The Taskbar is found.
Console.WriteLine("Can't proceed, Windows Explorer is currently running. Exiting...")
Environment.Exit(2)
End Select
End Sub
#End Region
End Module

At times Lego gets tied up with real life, and he is the only developer, so it might be awhile before a further update.  The time between updates sometimes varies wildly.  Since you are "desperate", you can help find the problem if you can do some more test runs.
 
1. Make a build just like the one that causes problems, but use an older version of Win Toolkit, so we can see at what point Win Toolkit changed to cause your issue.
2. Make a build with the latest version of Win Toolkit, but without any silent installers, just to see what happens.
3. Assuming (2) works, slowly add a few silent installers at a time to see if the problem might be related to a particular silent installer.  I'm not saying that would mean that it is that silent installer's fault, but it could point to some kind of dependency issue or something.
4. If (2) doesn't work, make a build without any tweaks.  Then slowly add them back in as in (3).
 
Bottom line, you want to try and determine if the problem occurs only with a particular installer, or tweak, or group of installers, or if it occurs with any installer no matter which one or how many.  Same with the tweaks you use.  If none of those tests provide any resolution, the only other thing you can try is to do the same kind of thing with your updates you integrate to see if one of them works better being installed at RunOnce.
 
Upload any logs created and provide a link to them here.  I know it's a lot of work, but the more testing and info you can provide the more likely the true problem can be resolved sooner.  Anything you can do will help.
 
Cheers and Regards

Please consider that you are using Windows 8.1!
 
May be the NSIS-Error is OS-dependent too.
 
Thiersee