I believe that IIS runs as 32-bit (WOW) on Windows Server 2003 x64. I don't think it's IIS causing this problem.
However, ASP.NET runs separately and you need to configure it as required in either 32-bit or 64-bit mode.
You might check this out: 32-bit DLLs go in a different place in Windows x64 and require some special commands to register them. I'm not 100% sure of how this works but that is a start!
I hope this helps!