I removed IIS and reinstalled it, that seems to have solved whatever the problem was.

is there a location to get the original install for this version?

I am getting this on our dev machine. Installing the latest version of the installer for CMS 6 R2 (from this monday) did not help. Same problem :( Reinstalling IIS is not an option. Any ideas?

http://world.episerver.com/Download/Categories/Products/EPiServer-CMS/

I wonder if it is because we have so many sites stopped? I will need to investigate further and get this to work asap. If I find the solution I will post it. Anyone with ideas?

From the log:

EPiServerInstall Information: 0 : Starting in C:\Windows\system32 with "C:\Program Files (x86)\EPiServer\Shared\Install\EPiServerInstall.exe" , 
EPiServerInstall Information: 0 : EPiServerInstall.exe started with arguments "", 
EPiServerInstall Information: 0 : Displaying Deployment Center, 
EPiServerInstall Information: 0 : Initializing... , 
EPiServerInstall Information: 0 : Popuplating sites... , 

The exception:

See the end of this message for details on invoking 
just-in-time (JIT) debugging instead of this dialog box.

************** Exception Text **************
System.NullReferenceException: Object reference not set to an instance of an object.
   at EPiServer.Install.IIS7.WebApplication.Initialize(Site site, Application application, InstallationManager installationManager)
   at EPiServer.Install.IIS7.WebApplication.<GetSites>d__9.MoveNext()
   at System.Linq.Buffer`1..ctor(IEnumerable`1 source)
   at System.Linq.OrderedEnumerable`1.<GetEnumerator>d__0.MoveNext()
   at EPiServer.Install.UI.Controls.WebServerTreeView.PopulateTree(Func`2 shouldListApplication)
   at EPiServer.Install.UI.RunScriptForm.PopulateSiteActions()
   at EPiServer.Install.UI.RunScriptForm.RunScriptForm_Load(Object sender, EventArgs e)
   at System.Windows.Forms.Form.OnLoad(EventArgs e)
   at System.Windows.Forms.Form.OnCreateControl()
   at System.Windows.Forms.Control.CreateControl(Boolean fIgnoreVisible)
   at System.Windows.Forms.Control.CreateControl()
   at System.Windows.Forms.Control.WmShowWindow(Message& m)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.ScrollableControl.WndProc(Message& m)
   at System.Windows.Forms.ContainerControl.WndProc(Message& m)
   at System.Windows.Forms.Form.WmShowWindow(Message& m)
   at System.Windows.Forms.Form.WndProc(Message& m)
   at System.Windows.Forms.Control.ControlNativeWindow.OnMessage(Message& m)
   at System.Windows.Forms.Control.ControlNativeWindow.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)


************** Loaded Assemblies **************
mscorlib
    Assembly Version: 2.0.0.0
    Win32 Version: 2.0.50727.5448 (Win7SP1GDR.050727-5400)
    CodeBase: file:///C:/Windows/Microsoft.NET/Framework/v2.0.50727/mscorlib.dll
----------------------------------------
EPiServerInstall
    Assembly Version: 1.1.464.0
    Win32 Version: 1.1.464.0
    CodeBase: file:///C:/Program%20Files%20(x86)/EPiServer/Shared/Install/EPiServerInstall.exe
----------------------------------------
System.Windows.Forms
    Assembly Version: 2.0.0.0
    Win32 Version: 2.0.50727.5446 (Win7SP1GDR.050727-5400)
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/System.Windows.Forms/2.0.0.0__b77a5c561934e089/System.Windows.Forms.dll
----------------------------------------
System
    Assembly Version: 2.0.0.0
    Win32 Version: 2.0.50727.5453 (Win7SP1GDR.050727-5400)
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/System/2.0.0.0__b77a5c561934e089/System.dll
----------------------------------------
System.Drawing
    Assembly Version: 2.0.0.0
    Win32 Version: 2.0.50727.5420 (Win7SP1.050727-5400)
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/System.Drawing/2.0.0.0__b03f5f7f11d50a3a/System.Drawing.dll
----------------------------------------
System.Configuration
    Assembly Version: 2.0.0.0
    Win32 Version: 2.0.50727.5420 (Win7SP1.050727-5400)
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/System.Configuration/2.0.0.0__b03f5f7f11d50a3a/System.Configuration.dll
----------------------------------------
System.Xml
    Assembly Version: 2.0.0.0
    Win32 Version: 2.0.50727.5420 (Win7SP1.050727-5400)
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/System.Xml/2.0.0.0__b77a5c561934e089/System.Xml.dll
----------------------------------------
System.Core
    Assembly Version: 3.5.0.0
    Win32 Version: 3.5.30729.5420 built by: Win7SP1
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/System.Core/3.5.0.0__b77a5c561934e089/System.Core.dll
----------------------------------------
EPiServerInstall.Common.1
    Assembly Version: 1.1.464.0
    Win32 Version: 1.1.464.0
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/EPiServerInstall.Common.1/1.1.464.0__8fe83dea738b45b7/EPiServerInstall.Common.1.dll
----------------------------------------
System.Xml.Linq
    Assembly Version: 3.5.0.0
    Win32 Version: 3.5.30729.5420 built by: Win7SP1
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/System.Xml.Linq/3.5.0.0__b77a5c561934e089/System.Xml.Linq.dll
----------------------------------------
Microsoft.Web.Administration
    Assembly Version: 7.0.0.0
    Win32 Version: 6.1.7601.17514
    CodeBase: file:///C:/Windows/assembly/GAC_MSIL/Microsoft.Web.Administration/7.0.0.0__31bf3856ad364e35/Microsoft.Web.Administration.dll
----------------------------------------

************** JIT Debugging **************
To enable just-in-time (JIT) debugging, the .config file for this
application or computer (machine.config) must have the
jitDebugging value set in the system.windows.forms section.
The application must also be compiled with debugging
enabled.

For example:

<configuration>
    <system.windows.forms jitDebugging="true" />
</configuration>

When JIT debugging is enabled, any unhandled exception
will be sent to the JIT debugger registered on the computer
rather than be handled by this dialog box.

Hi John,

I would use reflector to see what the Initialize site function does and try to make a powershell script that mimics that and debug it. To me it looks like it iterate through every site in the IIS and get some basic facts about them, e.g. the port and the applications.