I have just created an ASP.NET C# project and a virtual directory for it in IIS in (as far as I know) the normal way, but I am seeing very strange behavior that I have never see
I get the runtime error on a semi-regular basis; clearing out:
C:\Documents and Settings\\Local Settings\Application Data\Microsoft\WebsiteCache C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\Temporary ASP.NET Files
(obviously substitute your ) and running iisreset usually does the job for me. Also, try 'cleaning' the solution before you rebuild; sometimes appears to make a difference.
If you're still getting the same problem, try dropping and recreating the reference to the DLL.
Nothing too prescriptive I'm afraid but should hopefully get the job done!