I have come to a solution. In the end it was mostly a permissions issue. The 4 dlls also use a file called system.dna which seems to act as a config file, but more advanced. When the dlls load correctly the system doesn't access them at all, only the system.dna. I know this sounds strange.... but...

I've got an IIS v6 (Windows Server 2003) web site which uses some old DLL written with unmanaged code. (Aspx, C# using System.Runtime.InteropService to call unmanaged dll) But I've bought a new Windows Server 2008 with IIS7 and call to unmanaged DLL is not working. In fact my C# code call an...