I know not to put strongly named assemblies into the bin folder on early versions of ASP.NET. I remember this caused problems, but I don't remember specifically what problems. Does anyone know if this still applies to ASP.NET 2.0? Is there any reason not to put strongly named assemblies into the bin folder on ASP.NET 2.0 or later versions?
The problem you describe was fixed on .NET 2.0, so you don't need to worry about it anymore.
However, beware that if you put a strong-named assembly in the bin folder, and an assembly with the same strong name exists in the GAC, then the assembly in the GAC will get loaded.