i have just upgraded a test copy of my site to asp.net 4.0 and have noticed a strange issue that only arises when i upload the site to my server.
the site has an asm
Are you sure .NET 4 is installed on your server?
The ScriptHandlerFactory's "type" string in .NET 4 is:
System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=4.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35"
ASP.NET 4 now includes that in its default web.config at the machine level. So, you shouldn't need any mapping to the ScriptHandlerFactory in your project's web.config, 3.5 or 4.