I tend to use FireBug in Firefox - it allows you to see the contents of each dynamic .js file - you'll probably find that one of them is producing either a 404 or a 500 Internal Server Error.
Without knowing which AJAX framework you're using, I can't really help all that much, but I'd take a look at the httpHandlers declared in the web.config, you should probably see some entries like:
<httpHandlers>
<remove verb="*" path="*.asmx" />
<add verb="*" path="*.asmx" validate="false" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add verb="*" path="*_AppService.axd" validate="false" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add verb="GET,HEAD" path="ScriptResource.axd" type="System.Web.Handlers.ScriptResourceHandler, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" validate="false" />
<add verb="*" path="*.mvc" validate="false" type="System.Web.Mvc.MvcHttpHandler, System.Web.Mvc, Version=1.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
</httpHandlers>
These are for the standard .NET 3.5 script libraries, yours may well be different.
But take a look in there, and ensure that the libraries referenced are available - compare this section with the same section from the original 1.1 web.config - that should get you on the right track.