After upgrading to .Net 4.0, I'm getting the exception "Could not load file or assembly 'System.Windows, Version=2.0.5.0'" - asp.net-4.0

Question

We recently upgraded our web app from 3.5 to 4.0. Now after I login and load a page with Microsoft ScriptManager on it, I get:
Could not load file or assembly 'System.Windows, Version=2.0.5.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e' or one of its dependencies. The system cannot find the file specified.
It only happens the first time, reload the page and everything works.
UPDATE: We have all Silverlight v4 projects.I found the System.Windows.dll in the C:\Program Files\Reference Assemblies\Microsoft\Framework\Silverlight\v4.0 directory. Why would it look for version 2.0?
Here's the entire exception (edited and removed folder paths)
Server Error in '/test' Application.
Could not load file or assembly 'System.Windows, Version=2.0.5.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e' or one of its dependencies. The system cannot find the file specified.
Description: An unhandled exception occurred during the execution of the current web request. Please review the stack trace for more information about the error and where it originated in the code.
Exception Details: System.IO.FileNotFoundException: Could not load file or assembly 'System.Windows, Version=2.0.5.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e' or one of its dependencies. The system cannot find the file specified.
Source Error:
Line 450: <UC5:PageTitle ID="PageTitle" runat="server" />
Line 451: <UC2:PageTabs ID="testPageTabs" runat="server" />
Line 452: <asp:ScriptManager ID="ScriptManager1" runat="server"/>
Line 453: <div id="step1Div" style="padding-top: 10px; padding-left: 10px" runat="server">
Line 454: <asp:ValidationSummary ID="displayValidationSummary" ValidationGroup="displayCreateEditValidationGroup" runat="server" />
Source File: c:{directories}\Pages\Administration\DisplayCreateEdit.aspx Line: 452
Assembly Load Trace: The following information can be helpful to determine why the assembly 'System.Windows, Version=2.0.5.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e' could not be loaded.
WRN: Assembly binding logging is turned OFF.
To enable assembly bind failure logging, set the registry value [HKLM\Software\Microsoft\Fusion!EnableLog] (DWORD) to 1.
Note: There is some performance penalty associated with assembly bind failure logging.
To turn this feature off, remove the registry value [HKLM\Software\Microsoft\Fusion!EnableLog].
Stack Trace:
[FileNotFoundException: Could not load file or assembly 'System.Windows, Version=2.0.5.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e' or one of its dependencies. The system cannot find the file specified.]
System.ModuleHandle.ResolveType(RuntimeModule module, Int32 typeToken, IntPtr* typeInstArgs, Int32 typeInstCount, IntPtr* methodInstArgs, Int32 methodInstCount, ObjectHandleOnStack type) +0
System.ModuleHandle.ResolveTypeHandleInternal(RuntimeModule module, Int32 typeToken, RuntimeTypeHandle[] typeInstantiationContext, RuntimeTypeHandle[] methodInstantiationContext) +180
System.Reflection.RuntimeModule.ResolveType(Int32 metadataToken, Type[] genericTypeArguments, Type[] genericMethodArguments) +192
System.Reflection.CustomAttribute.FilterCustomAttributeRecord(CustomAttributeRecord caRecord, MetadataImport scope, Assembly& lastAptcaOkAssembly, RuntimeModule decoratedModule, MetadataToken decoratedToken, RuntimeType attributeFilterType, Boolean mustBeInheritable, Object[] attributes, IList derivedAttributes, RuntimeType& attributeType, IRuntimeMethodInfo& ctor, Boolean& ctorHasParameters, Boolean& isVarArg) +115
System.Reflection.CustomAttribute.GetCustomAttributes(RuntimeModule decoratedModule, Int32 decoratedMetadataToken, Int32 pcaCount, RuntimeType attributeFilterType, Boolean mustBeInheritable, IList derivedAttributes, Boolean isDecoratedTargetSecurityTransparent) +426
System.Reflection.CustomAttribute.GetCustomAttributes(RuntimeAssembly assembly, RuntimeType caType) +103
System.Reflection.RuntimeAssembly.GetCustomAttributes(Boolean inherit) +33
System.Web.UI.AssemblyCache.GetAjaxFrameworkAssemblyAttribute(Assembly assembly) +76
System.Web.UI.ScriptManager.get_DefaultAjaxFrameworkAssembly() +388
System.Web.UI.ScriptManager..ctor() +26
ASP.pages_administration_displaycreateedit_aspx.__BuildControlScriptManager1() in c:{directories}\Pages\Administration\DisplayCreateEdit.aspx:452
ASP.pages_administration_displaycreateedit_aspx.__BuildControlContent1(Control __ctrl) in c:{directories}\Pages\Administration\DisplayCreateEdit.aspx:9
System.Web.UI.CompiledTemplateBuilder.InstantiateIn(Control container) +12
System.Web.UI.MasterPage.InstantiateInContentPlaceHolder(Control contentPlaceHolder, ITemplate template) +87
ASP.master_master.__BuildControlContentPlaceHolder1() in c:{directories}\Master.master:28
ASP.master_master.__BuildControlmasterForm() in c:{directories}\Master.master:13
ASP.master_master.__BuildControlTree(master_master __ctrl) in c:{directories}\Master.master:1
ASP.master_master.FrameworkInitialize() in c:\WINDOWS\Microsoft.NET\Framework\v4.0.30319\Temporary ASP.NET Files\zoning\dff1a5fe\99aa3a7f\App_Web_shgw15qp.4.cs:0
System.Web.UI.UserControl.InitializeAsUserControlInternal() +35
System.Web.UI.MasterPage.CreateMaster(TemplateControl owner, HttpContext context, VirtualPath masterPageFile, IDictionary contentTemplateCollection) +8832342
System.Web.UI.Page.get_Master() +54
System.Web.UI.Page.ApplyMasterPage() +15
System.Web.UI.Page.PerformPreInit() +45
System.Web.UI.Page.ProcessRequestMain(Boolean includeStagesBeforeAsyncPoint, Boolean includeStagesAfterAsyncPoint) +328
Version Information: Microsoft .NET Framework Version:4.0.30319; ASP.NET Version:4.0.30319.1
And the system.web of our web.config:
<system.web>
<pages validateRequest="false" buffer="true" theme="Summer" controlRenderingCompatibilityVersion="3.5" clientIDMode="AutoID">
<controls>
<add namespace="AjaxControlToolkit" assembly="AjaxControlToolkit" tagPrefix="ajaxToolkit"/>
</controls>
<tagMapping>
<add tagType="System.Web.UI.WebControls.TextBox" mappedTagType="CleanTextBox"/>
<add tagType="System.Web.UI.HtmlControls.HtmlTextArea" mappedTagType="CleanTextArea"/>
</tagMapping>
</pages>
<compilation debug="true" targetFramework="4.0">
<assemblies>
</assemblies>
</compilation>
<authentication mode="Forms">
<forms requireSSL="false" cookieless="UseDeviceProfile" loginUrl="~/Pages/Authentication/Login.aspx" timeout="60" defaultUrl="~/Pages/Authentication/AccountHome.aspx" slidingExpiration="true" name="sqlAuthCookie" protection="All"/>
</authentication>
<sessionState timeout="60" mode="StateServer" stateConnectionString="tcpip=localhost" stateNetworkTimeout="60" cookieless="false"/>
<customErrors mode="RemoteOnly" defaultRedirect="~/Pages/Global/DefaultError.aspx">
<error statusCode="404" redirect="~/Pages/Global/404.htm"/>
<error statusCode="403" redirect="~/Pages/Global/403.htm"/>
</customErrors>
<httpHandlers>
<add path="*js.axd" verb="*" type="ScriptCompressorHandler"/>
<add path="*css.axd" verb="*" type="CssCompressorHandler"/>
<add path="*css" verb="*" type="CssCompressorHandler"/>
<add verb="*" path="Reserved.ReportViewerWebControl.axd" type="Microsoft.Reporting.WebForms.HttpHandler, Microsoft.ReportViewer.WebForms, Version=9.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a"/>
</httpHandlers>
<httpModules>
<remove name="WindowsAuthentication"/>
<remove name="PassportAuthentication"/>
<remove name="AnonymousIdentification"/>
<remove name="RoleManager"/>
<remove name="Profile"/>
<remove name="ErrorHandlerModule"/>
<add type="ScriptCompressorModule" name="ScriptCompressorModule"/>
<add type="CssCompressorModule" name="CssCompressorModule"/>
</httpModules>
<machineKey validationKey="{key}" decryptionKey="{key}" validation="SHA1"/>
<httpRuntime maxRequestLength="1048576" executionTimeout="3600" requestValidationMode="2.0"/>
</system.web>
See the same problem here and Microsoft Feedback/Bug report
Edit: I'm running VS 2010, XP with IIS 5.0 (I miss Win 7 at work every day :-)). We have the web app running under the local IIS instance, not Cassini. We deployed it to a test server and I did not see the exception. After I installed the C:\Program Files\Reference Assemblies\Microsoft\Framework\Silverlight\v4.0\System.windows.dll to the GAC and then removed it and haven't seen the same exception, though my colleague hasn't done this and still sees it occasionally. I think it only happens when the app is restarted (which happens every time we rebuild the app when developing locally).

Answer 1

Sounds like one of the projects in your solution is referencing the v2 system assemblies. Make sure that all of your projects and application pools are set to use 4.0. You can set this in the project properties in Visual Studio.
(Note that you'll have to rebuild your solution with the new settings if you haven't already).

Answer 2

I have been having the same issues for a long time, but just found some old Silverlight Assemblies in my bin folder, removed those and voila.. error gone

Answer 3

Adding reference to AjaxControlToolkit.dll and adding the header
<%# Register Assembly="AjaxControlToolkit" Namespace="AjaxControlToolkit" TagPrefix="asp" %>
to the aspx that contains the script manager solved the problem for me.