WebResource.axd is an HTTP Handler and it's mapped to IIS without a file requirement - ASP.NET generates the response for this. I doubt the error you are getting is related to the AXD file not firing - ASP.NET uses this resource handler in many places.
There's something else going on.
+++ Rick ---
>>Not in a position to check this at the moment but I thing the .AXD extension is a HTTPHandler (see if it's in Configuration Mappings in IIS).
>
>Yes, but if the file is not there, it will never work. I also checked in the .NET Framework to locate such a file and was not able to find one.