This has cost me many pained hours so I thought I would share it as I did not see any posts that had the scenario/troubles I had.

Basically I am on DNN 4.9.4 using the old version of the MS AJAXToolkit for .NET 2.0. For various reasons (AJAX errors in certain scenarios in IE) I wanted to upgrade to the latest AJAXToolkit (the .NET 2.0 version is almost 2 years old!).

These are the steps I took (I assume your machine has .NET 3.5 SP1 installed):

1. Updated my web.config to use 3.5 (I used Michael's LinqPrep module as I was in a rush
2. Checked my site - everything (except IdentitySwitcher) seems to work ok
3. I then downloaded the latest AJAXToolkit (Sept 2009) for 3.5 and this is where it all went wrong ;)
4. I deleted the old AjaxControlToolkit.dll in my website bin and anywhere else it was. I then overwrote it with the new 3.5 version and tried to compile.
5. I got this error in VS 2008 - "Error 1 Assembly 'AjaxControlToolkit, Version=3.0.30512.20315, Culture=neutral, PublicKeyToken=28f01b0e84b6d53e' uses 'System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35' which has a higher version than referenced assembly 'System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35"
6. After a lot of searching/reading it seemed as though all posts were saying you had to edit your web.config to update your reference. I thought this was strange as there is no web.config in my WAP projects. I edited the website w.c.
7. It seems as though the System.Web.Extensions, Version=3.5.0.0 needs to be changed manually in the web.config, so I updated these all (from the old 1.x version) - there were 8 in my W.C
8. As I suspected this had no affect on my 2008 complie errors. I opened notepad and examined the project file and found a reference to the old version (something like this: "Reference Include="System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL" HintPath>..\..\..\..\WINDOWS\assembly\GAC_MSIL\System.Web.Extensions\1.0.61025.0__31bf3856ad364e35\System.Web.Extensions.dll/HintPath
    
9. I changed this in Notepad and closed and open the solution and finally the porject built! It all seems to work now...
10. When I moved to the live site it fell over so I had to add this to my web.config:      <runtime>
            <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
                <dependentAssembly>
                    <assemblyIdentity name="System.Web.Extensions" publicKeyToken="31bf3856ad364e35"/>
                    <bindingRedirect oldVersion="1.0.0.0-1.1.0.0" newVersion="3.5.0.0"/>
                </dependentAssembly>
                <dependentAssembly>
                    <assemblyIdentity name="System.Web.Extensions.Design" publicKeyToken="31bf3856ad364e35"/>
                    <bindingRedirect oldVersion="1.0.0.0-1.1.0.0" newVersion="3.5.0.0"/>
                </dependentAssembly>
            </assemblyBinding>
        </runtime>

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